Modeling Habitat Capacity and Population Productivity for Spring-run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Technical Report

Prepared for National Marine Fisheries Service 777 Sonoma Avenue, Suite 325 Santa Rosa, California 95404

Prepared by Stillwater Sciences 2855 Telegraph Ave., Suite 400 Berkeley, California 94705

February 2012

Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Suggested citation: Stillwater Sciences. 2012. Modeling habitat capacity and population productivity for spring-run Chinook salmon and steelhead in the Upper Yuba River watershed. Technical Report. Prepared by Stillwater Sciences, Berkeley, California for National Marine Fisheries Service, Santa Rosa, California.

February 2012 Stillwater Sciences i Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table of Contents

EXECUTIVE SUMMARY...... ES-1

1 INTRODUCTION ...... 1

1.1 Goals and Objectives ...... 1 1.2 Approach...... 1 1.3 Basin Overview...... 2

2 FOCAL SPECIES...... 5

2.1 Spring-run Chinook Salmon ...... 5 2.1.1 Status and life history...... 5 2.1.2 Conceptual model of key limiting factors ...... 7 2.2 Steelhead...... 8 2.2.1 Status and life history...... 8 2.2.2 Conceptual model of key limiting factors ...... 10

3 RIPPLE MODEL OVERVIEW ...... 11

4 MODELED SUB-BASINS AND ALTERNATIVE MANAGEMENT SCENARIOS ....12

4.1 Sub-basins...... 12 4.2 Modeling Scenarios ...... 14 4.2.1 Current conditions...... 16 4.2.1.1 Spring-run Chinook salmon...... 16 4.2.1.2 Steelhead...... 18 4.2.2 Alternative Management Scenario 1 ...... 20 4.2.2.1 Spring-run Chinook salmon...... 20 4.2.2.2 Steelhead...... 21 4.2.3 Alternative Management Scenario 2 ...... 23 4.2.3.1 Spring-run Chinook salmon...... 23 4.2.3.2 Steelhead...... 24 4.3 Expanded Steelhead Distribution...... 24 4.3.1 Current conditions...... 25 4.3.2 Alternative Management Scenarios 1 and 2...... 26

5 STREAM CHANNEL NETWORK AND HYDRAULIC GEOMETRY ...... 27

5.1 Stream Channel Network Development and Attribution...... 27 5.2 Hydraulic Geometry ...... 28 5.2.1 Current conditions in the upper Yuba River watershed ...... 28 5.2.1.1 North Yuba sub-basin ...... 30 5.2.1.2 Middle Yuba and South Yuba sub-basins...... 32 5.2.1.3 Below New Bullards Bar Dam ...... 34 5.2.2 Alternative management scenarios...... 34 5.3 Application of GEO Module Results...... 36

February 2012 Stillwater Sciences ii Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

6 SPRING-RUN CHINOOK SALMON ...... 37

6.1 Habitat Capacity (HAB) ...... 37 6.1.1 Methods...... 37 6.1.1.1 Channel gradient and habitat type composition...... 37 6.1.1.2 Holding density and usable fraction...... 38 6.1.1.3 Spawning density and usable fraction...... 39 6.1.1.4 Juvenile rearing density and usable fraction...... 40 6.1.1.5 Physical habitat thresholds...... 42 6.1.1.6 Parameterization of Alternative Management Scenarios...... 42 6.1.2 Results and discussion...... 42 6.1.2.1 Predicted distribution of suitable habitat ...... 42 6.1.2.2 Carrying capacity estimates ...... 43 6.2 Population Dynamics (POP)...... 46 6.2.1 POP module structure...... 46 6.2.2 POP module parameterization...... 49 6.2.3 Results and discussion...... 49 6.3 Chinook Salmon Model Sensitivity and Uncertainty ...... 52

7 STEELHEAD...... 53

7.1 Model Assumptions and Structure...... 53 7.2 Habitat Capacity (HAB) ...... 54 7.2.1 Methods...... 54 7.2.1.1 Channel gradient and habitat type composition...... 54 7.2.1.2 Spawning density and usable fraction...... 55 7.2.1.3 Summer juvenile rearing density and usable fraction...... 56 7.2.1.4 Winter juvenile rearing density and usable fraction ...... 58 7.2.1.5 Physical habitat thresholds...... 59 7.2.1.6 Parameterization of Alternative Management Scenarios...... 60 7.2.2 Results and discussion...... 60 7.2.2.1 Predicted distribution of suitable habitat ...... 60 7.2.2.2 Carrying capacity estimates ...... 62 7.3 Smolt Production Estimates...... 65 7.3.1 Methods...... 65 7.3.2 Results and discussion...... 65 7.4 Steelhead—Model Sensitivity and Uncertainty...... 67

8 MODEL CONSIDERATIONS ...... 67

8.1 Modeling Challenges ...... 68 8.2 Model Validation ...... 68 8.3 Recommendations for Model Refinement ...... 69

9 REFERENCES...... 70

February 2012 Stillwater Sciences iii Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Tables Table 2-1. Water temperature criteria for spring-run Chinook salmon in the upper Yuba River watershed...... 5 Table 2-2. Water temperature criteria for steelhead in the upper Yuba River watershed ...... 9 Table 4-1. Characteristics of modeled sub-basins of the upper Yuba River watershed...... 13 Table 4-2. Mainstem fish passage barriers in the upper Yuba River watershed...... 13 Table 4-3. Spring-run Chinook salmon habitat predicted under each modeling scenario in sub- basins of the upper Yuba River watershed...... 15 Table 4-4. Steelhead habitat predicted under each modeling scenario in sub-basins of the upper Yuba River watershed...... 16 Table 4-5. Comparison of steelhead habitat predicted in the mainstems of the South and Middle Yuba rivers using a ≤ 20°C MWAT criterion vs. higher water temperature criteria based on observed rainbow trout distribution...... 26 Table 5-1. Hydraulic geometry relationships for the SY, MY, NY, and NBB sub-basins under current conditions...... 29 Table 6-1. Input parameters for the HAB module...... 37 Table 6-2. Mean sizes of spring-run Chinook salmon redds...... 39 Table 6-3. Summer rearing densities reported for age-0 spring-run Chinook salmon...... 41 Table 6-4. Parameters changed in the HAB module for spring-run Chinook salmon model runs for Alternative Management Scenarios 1 and 2 relative to current conditions.. 42 Table 6-5. Predicted habitat carrying capacities of spring-run Chinook salmon holding, spawning, and summer rearing life stages for each modeled sub-basin and scenario in the upper Yuba River watershed...... 44 Table 6-6. Life stages represented in the spring-run Chinook salmon POP module...... 47 Table 6-7. Predicted equilibrium population sizes for select spring-run Chinook salmon life stages for each modeled sub-basin and scenario in the upper Yuba River watershed...... 49 Table 6-8. Percent of total predicted spring-run Chinook salmon juvenile production composed of efry, smolt0, and smolt1 life history types for each modeled reach and scenario in the upper Yuba River watershed...... 52 Table 7-1. Habitat type-specific summer rearing densities reported for age 1+ juvenile steelhead...... 56 Table 7-2. Winter rearing densities reported for juvenile steelhead...... 59 Table 7-3. Parameters changed in the HAB module for steelhead model runs for Alternative Management Scenarios 1 and 2 relative to current conditions...... 60 Table 7-4. RIPPLE-predicted habitat carrying capacities for steelhead life stages for each modeled reach and scenario in the upper Yuba River watershed...... 62 Table 7-5. Comparison of predicted habitat carrying capacities for steelhead life stages using 20°C and higher water temperature criteria to define extent of suitable habitat...... 64 Table 7-6. Steelhead smolt production estimates based on RIPPLE-predicted summer carrying capacities for age 1+ steelhead for each modeled sub-basin and scenario in the upper Yuba River watershed...... 66

February 2012 Stillwater Sciences iv Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Figures Figure 1-1. Hydrographs for the South, Middle, and North Yuba rivers for the overlapping period of record...... 4 Figure 4-1. Miles of stream thermally suitable for spring-run Chinook salmon holding in the mainstem and tributaries of each modeled sub-basin under current conditions and two modeled scenarios...... 20 Figure 4-2. Miles of stream thermally suitable for steelhead summer rearing and spawning in the mainstem and tributaries of each modeled sub-basin under current conditions and two modeled scenarios...... 22 Figure 5-1. Hydraulic geometry relationships for bankfull width and depth in the NY sub-basin...... 30 Figure 5-2. Hydraulic geometry relationships for winter baseflow and summer low flow widths in the NY sub-basin...... 31 Figure 5-3. Hydraulic geometry relationship for summer low flow depths in the NY sub-basin. 31 Figure 5-4. Hydraulic geometry relationships for bankfull width and depth in the MY and SY sub-basins under current conditions...... 33 Figure 5-5. Hydraulic geometry relationships for winter baseflow and summer low flow widths in the MY and SY sub-basins under current conditions...... 33 Figure 5-6. Hydraulic geometry relationship for summer low flow depths in the MY and SY sub-basins under current conditions...... 34 Figure 5-7. Hydraulic geometry relationships for summer low flow width in the MY and SY sub-basins under alternative management scenarios...... 35 Figure 5-8. Hydraulic geometry relationships for summer low flow depth in the MY and SY sub-basins under alternative management scenarios...... 36 Figure 6-1. Predicted habitat carrying capacity of spring-run Chinook salmon redds under current conditions and two modeled scenarios...... 45 Figure 6-2. Schematic diagram showing the relationships between each life stage in the POP module and the point at which each carrying capacity is applied to the population.. 47 Figure 6-3. Predicted equilibrium population sizes for different aged spring-run Chinook salmon smolts under current conditions and two modeled scenarios...... 51 Figure 7-1. Number of steelhead redds predicted under current conditions and two modeled scenarios...... 63

Maps Map 1. Modeled sub-basins of the upper Yuba River watershed. Map 2. Contributing drainage areas for channels in the upper Yuba River watershed. Map 3. Channel gradients in the upper Yuba River watershed. Map 4. Extent of predicted holding and summer rearing habitat for spring-run Chinook salmon in the upper Yuba River watershed under current conditions and Alternative Management Scenarios 1 and 2. Map 5. Extent of predicted spawning and summer rearing habitat for steelhead in the upper Yuba River watershed under current conditions and Alternative Management Scenarios 1 and 2, using a 20°C water temperature criterion to define suitable habitat. Map 6. Extent of predicted spawning and summer rearing habitat for steelhead in the upper Yuba River watershed under current conditions and Alternative Management Scenarios 1 and 2, using 25.2°C and 23.2°C water temperature criteria to define suitable habitat in the South Yuba and Middle Yuba sub-basins, respectively.

February 2012 Stillwater Sciences v Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Appendices Appendix A. Meteorological and Streamflow Conditions Compared to Historical Averages Appendix B. HFAM Water Temperature Model Output for the South Yuba and Middle Yuba Rivers Appendix C. 2010 Water Temperature Data for the North Yuba River Appendix D. GEO Module Methods Tables Appendix E. North Yuba Sub-basin Channel Geometry and Habitat Type Data Appendix F. Spring-run Chinook Salmon HAB Module Methods and Tables Appendix G. Spring-run Chinook Salmon POP Module Methods and Tables Appendix H. Steelhead HAB Module Methods and Tables

February 2012 Stillwater Sciences vi Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

EXECUTIVE SUMMARY

As part of the Habitat Assessment and Reintroduction Implementation Plan for Central Valley spring-run Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss), the National Marine Fisheries Service (NMFS) contracted Stillwater Sciences to develop an exploratory application of the spatially explicit model, RIPPLE, to quantify habitat carrying capacity and freshwater productivity potential for these two salmonid species in the upper Yuba River watershed. The following report describes the methods and results of that effort. Using a compilation of physical and biological data from field studies, literature review and scientific consultation, RIPPLE was parameterized to simulate the carrying capacity of current conditions for spring-run Chinook salmon and steelhead, along with the productivity potential for spring-run Chinook salmon. Estimates of current conditions are contrasted with simulated future conditions resulting from potential flow, temperature, and habitat enhancements. Data sources, model sensitivity, and parameter uncertainty are documented in the report, along with discussions of model challenges and future recommendations for validation and refinement.

Basin Overview and Focal Species Basin overview The Yuba River is a tributary to the Feather River, a major Sacramento River tributary in California’s Central Valley. The upper Yuba River watershed extends from the crest of the Sierra Nevada (elevation 2,774 m [9,100 ft]) to Englebright Dam (elevation 161 m [527 ft]). The upper Yuba River watershed is drained by three major tributaries: the South Yuba River, the Middle Yuba River, and the North Yuba River. Flows in the South Yuba and Middle Yuba rivers are largely regulated by dams and associated water conveyance facilities, whereas the North Yuba River is unregulated upstream of New Bullards Bar Dam. Englebright Dam, located on the mainstem Yuba River 23.4 river miles (RM) upstream of its confluence with the Feather River, is a complete barrier to fish passage. New Bullards Bar Dam on the North Yuba River and Our House Dam on the Middle Yuba River are also complete barriers to fish passage. Prior to the construction of dams in the basin, the South Yuba, Middle Yuba, and North Yuba rivers are believed to have provided prime habitat for spring-run Chinook salmon and steelhead. Both of these species currently occur in the lower Yuba River below Englebright Dam.

The upper Yuba River watershed has a Mediterranean climate, with cool, wet winters and hot, dry summers. Stream flows in the upper Yuba River are characterized by low and constant summer flows (generally mid-July through October), winter storm peaks, and spring snowmelt runoff. The river channels in the upper Yuba River watershed are deeply incised, with alternating bedrock and alluvial reaches. A variety of native resident fish species, including rainbow trout (Oncorhynchus mykiss), are present in the upper Yuba River watershed, as well as several non- native fish species.

Focal species The lower Yuba River supports anadromous fish species including spring-run Chinook salmon in the California Central Valley Evolutionarily Significant Unit (ESU) and steelhead in the California Central Valley Distinct Population Segment (DPS). Both populations are listed as threatened under the federal Endangered Species Act.

February 2012 Stillwater Sciences ES-1 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Adult spring-run Chinook salmon enter Sacramento River tributaries primarily from April through June as sexually immature fish and hold in deep, cold pools for several months before spawning. Evidence indicates that holding adults can become physiologically stressed at water temperatures greater than 19°C. Spawning generally occurs between mid-August and October, peaking in September. In the Sacramento River basin, studies have shown that water temperatures greater than 15.6°C are usually stressful for spawning adults, and developing eggs require water temperatures less than 14.4° C for normal development. Spring-run Chinook salmon typically spend one year or more rearing in fresh water before migrating to sea. Although rearing juvenile spring-run Chinook salmon can survive for short periods in water temperatures up to 25°C, there is evidence that they can become physiologically stressed at temperatures above 18.3°C.

Adult steelhead migrate upstream into the Sacramento River during most months of the year, beginning in July, peaking in September, and continuing through February or March. Steelhead adults typically spawn in small streams and tributaries where cool, well-oxygenated water is available year-round. Spawning occurs from December through April, peaking from January though March. During egg incubation, steelhead require water temperatures less than 12.8°C to ensure successful embryonic development. After hatching, steelhead have a highly variable life history strategy. Juveniles may rear in fresh water for 2–4 years before emigrating to the ocean, typically from April–June. In the Sacramento River basin, steelhead generally emigrate as 2-year- olds during spring and early summer months. Juvenile steelhead generally require water temperatures lower than 20°C to avoid physiological stress; however, some strains of O. mykiss have been shown to grow well at temperatures as high as 22°C and maintain weight at temperatures as high as 25°C.

RIPPLE Model RIPPLE is a digital terrain-based model that predicts the distribution of fish habitat conditions throughout a watershed and simulates salmon population dynamics. It is a powerful tool for evaluating the effectiveness of restoration and recovery planning strategies. Developed in collaboration between Stillwater Sciences and UC Berkeley, RIPPLE characterizes the geomorphic and ecological processes that create and maintain freshwater salmon habitat. One of the guiding principles of RIPPLE is the assumption that physical processes and the resulting environment—specifically topography, geology, climate, drainage area, channel gradient, channel longitudinal profile—are essentially time invariant compared with ecosystems and the animal and plant populations supported by these ecosystems. This assumption enables us to construct a model that establishes a physical template composed of such information as topographic data, channel networks, and geology. RIPPLE uses geomorphic characteristics and physical habitat characteristics, combined with density and suitability criteria by species and life stage, to predict reach-specific historical, current, and potential future salmon habitat conditions. RIPPLE then employs a multi-stage, stock-production model to predict long-term average abundance for each life stage. Operationally RIPPLE is made up of three modules: 1. a physical module (“GEO”) that stratifies the channel network based on geomorphic and hydrological attributes (e.g., gradient, drainage area, bankful width and depth, summer low flow width and depth); 2. a habitat carrying capacity module (“HAB”) that defines the habitat quantity and quality for each reach, species and life stage; and

February 2012 Stillwater Sciences ES-2 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

3. a population dynamics module (“POP”) that employs biological parameters and stock- production relationships to estimate equilibrium population sizes at variable spatial scales and locations throughout the watershed.

RIPPLE is a flexible, scientifically rigorous tool designed for salmon conservation and management. Although the model is open-source and public domain, the spring-run Chinook and steelhead applications developed for the upper Yuba River watershed are not currently supported by a graphic user interface; therefore, model results cannot easily be publicly modified at the time of this publication.

Modeling Approach and Management Scenarios The upper Yuba River watershed, upstream of Englebright Dam, was divided into four separate sub-basins for modeling purposes: the South Yuba (SY), Middle Yuba (MY), and North Yuba (NY) river watersheds, and the watershed area between New Bullards Bar Dam and Englebright Reservoir (the NBB sub-basin). The sub-basins each have distinct attributes and physical habitat conditions that require different model parameters. Only a portion of the stream channel network in any sub-basin would be accessible to reintroduced spring-run Chinook salmon and steelhead and provide suitable habitat for these species. The upstream and downstream extent of potential habitat under each modeled scenario was defined for modeling purposes by applying four criteria: (1) known natural barriers, (2) channel gradient thresholds, (3) channel width thresholds, and (4) water temperature thresholds. For purposes of this assessment it was assumed that passage by salmon and steelhead would be possible in the mainstem reaches of each sub-basin up to existing natural passage barriers, and in smaller tributaries upstream to a point at which either channel gradient is too steep for passage or the channel is too narrow to provide suitable habitat.

For spring-run Chinook salmon, the upstream limit of potentially suitable habitat for all life stages was defined as any portion of the channel network with a gradient of 12% or greater, or with a sustained (> 300 m [984 ft]) gradient of 8% or greater. Channels with a summer low-flow width less than 8.5 m (28 ft) were assumed to be too narrow to provide suitable holding or spawning habitat. For steelhead, the upstream limit of potentially suitable habitat in tributaries in each sub-basin was defined as any portion of the channel network with a gradient of 20% or greater, or with a sustained (> 300 m [984 ft]) gradient of 8% or greater. Channels with a winter baseflow width less than 2 m (6.6 ft) were assumed to be too narrow to provide suitable steelhead spawning habitat. For modeling purposes it was assumed that rearing did not occur in reaches upstream of spawning.

Because the amount of suitable habitat for each species varies as a function of flow and related environmental conditions such as water temperature, a range of potential conditions, or scenarios, were modeled. The channel gradient and width thresholds described above were used to define the upstream extent of tributary habitat for all spring-run Chinook salmon and steelhead life stages in all sub-basins under all scenarios. The downstream extent of habitat was defined separately for different modeling scenarios.

In each sub-basin, current conditions were modeled to predict carrying capacity and production potential for both spring-run Chinook salmon and steelhead. Additionally, in the SY, MY, and NBB sub-basins, two alternative management scenarios were modeled that represent potential future conditions that could be realized by implementing flow and habitat enhancements. Because the North Yuba River upstream of New Bullards Bar Reservoir is unregulated, alternative flow management is not possible and alternative scenarios were not considered for the NY sub-basin.

February 2012 Stillwater Sciences ES-3 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Based on previous assessments of habitat conditions in the upper Yuba River watershed, the primary life stages of concern were adult holding for spring-run Chinook salmon and juvenile rearing for both spring-run Chinook salmon and steelhead. If reintroduction were to take place, these life stages would be present in the upper Yuba River watershed during the hottest months of the summer when water temperatures under current conditions reach or exceed critical thermal maxima for these species. The alternative management scenarios are therefore targeted toward reducing water temperatures in the critical summer months through additional instream flow releases below Project dams. In the NBB sub-basin, the alternative management scenarios also include augmenting spawning gravel, which is currently limited below New Bullards Bar Dam.

Current conditions The downstream extent of suitable spring-run Chinook salmon holding and rearing habitat under current conditions was defined by a water temperature suitability criterion (maximum weekly average temperature, or MWAT) of ≤ 19°C. For RIPPLE modeling purposes, we also used the 19°C MWAT to define the extent of thermally suitable habitat for rearing juvenile spring-run Chinook salmon. The locations at which these thermal suitability criteria were exceeded were estimated using measured or modeled water temperature data. Where the distance between data collection points was too large to provide useful spatial resolution in the water temperature data, linear interpolation was used to estimate the location at which the 19°C MWAT limit was likely exceeded. The downstream extent of spring-run Chinook salmon spawning habitat was modeled to extend a fixed distance of 3 miles downstream from holding habitat, based on evidence from the literature (though it was assumed that most post-holding movement will be upstream).

The downstream extent of suitable steelhead rearing habitat under current conditions was defined as the location in each mainstem river where the MWAT was measured or predicted to exceed 20°C. Where the distance between data collection points was too large to provide useful spatial resolution in the water temperature data, linear interpolation was used to estimate the location at which the 20°C MWAT water temperature threshold was likely exceeded. For modeling purposes, it was assumed that all accessible tributaries are thermally suitable for steelhead rearing. The downstream extent of potential spawning habitat in the SY, MY, and NY sub-basins under current conditions was assumed to be the same as the downstream extent of rearing habitat. This was based on the assumption that successful rearing depends on the availability of (thermally) suitable rearing habitat located downstream of spawning locations. For modeling purposes we assumed that rearing only occurs downstream of spawning. In the NBB sub-basin, potential spawning habitat in the mainstem Yuba River under current conditions was assumed to be present only downstream of New Colgate Powerhouse because of a lack of spawning gravel from New Bullards Bar Dam downstream to the powerhouse.

Alternative management scenarios Alternative Management Scenario 1 assumes that increased releases from dams in the SY, MY, and NBB sub-basins would increase the downstream extent of potential summer habitat for spring-run Chinook salmon and steelhead in these sub-basins compared with current conditions. Alternative Management Scenario 2 assumes that dam releases in the SY, MY, and NBB sub- basins would be greater than those under Scenario 1 and would further increase the downstream extent of potential summer habitat for spring-run Chinook salmon and steelhead in these sub- basins compared with Alternative Management Scenario 1. Scenario 2 also assumes that a gravel augmentation program would be implemented to restore mainstem spawning habitat to its approximate unimpaired extent in the NBB sub-basin downstream of New Bullards Bar Dam.

February 2012 Stillwater Sciences ES-4 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Expanded steelhead distribution The primary approach for defining suitable steelhead habitat was based on an assumed water temperature suitability criterion of ≤ 20°C MWAT for steelhead rearing. However, rainbow trout have been observed at relatively high densities in the South and Middle Yuba rivers considerably farther downstream than predicted based on this temperature criterion. It is possible that the use of a 20°C MWAT criterion results in a highly conservative estimate of steelhead habitat capacity, and that reintroduced steelhead could find suitable habitat where the MWAT is > 20°C. Therefore, a separate analysis was conducted to illustrate potential increases in steelhead habitat capacity and production in the South and Middle Yuba rivers that could result if observed rainbow trout distributions, and the associated water temperatures, were used to define the downstream extent of suitable steelhead habitat.

Spring-run Chinook Salmon Results Predicted distribution of suitable habitat In the SY sub-basin, under current conditions, no suitable spring-run Chinook salmon habitat was identified due to water temperature restrictions. In contrast, 7 miles of mainstem and 3.3 miles of tributary habitat were predicted to be suitable for holding, spawning, and summer rearing under Alternative Management Scenario 1. An additional 8.3 miles of mainstem habitat were predicted under Alternative Management Scenario 2. Suitable tributary habitat in the SY sub-basin did not change between the two Alternative Management Scenarios.

In the MY sub-basin, under current conditions, 2.3 miles of mainstem habitat were identified as suitable for spring-run Chinook holding, spawning, and summer rearing. In contrast, 11.9 miles of mainstem habitat were predicted to be suitable under Alternative Management Scenario 1 and an additional 10.6 miles of mainstem habitat were predicted under Alternative Management Scenario 2. No suitable tributary habitat in the MY sub-basin was identified for current conditions or either Alternative Management Scenario.

In the NY sub-basin, under current conditions, 27.7 miles of the mainstem and 7.0 miles of tributary habitat—considerably more than the SY and MY sub-basins—were identified as suitable habitat for spring-run Chinook salmon holding, spawning, and summer rearing. Alternative management scenarios were not modeled in the NY sub-basin.

In the NBB sub-basin, under current conditions, 3.2 miles of the mainstem North Yuba River was identified as suitable holding and summer rearing habitat for spring-run Chinook. However, due to lack of suitable spawning gravel in the mainstem between New Bullards Bar Dam and the Middle Yuba River confluence, spawning under current conditions was only predicted to occur downstream of New Colgate Powerhouse. Under Alternative Management Scenarios 1 and 2, which stipulate increased cold water releases from New Bullards Bar Dam and spawning gravel augmentation, the entire 10.3 miles of mainstem channel from New Bullards Bar Dam downstream to Englebright Reservoir were predicted to be suitable for spring-run Chinook salmon holding, spawning, and summer rearing. No suitable tributary habitat in the NBB sub- basin was identified for spring-run Chinook salmon under current conditions or either of the alternative management scenarios.

February 2012 Stillwater Sciences ES-5 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Carrying capacity estimates Results of the HAB module output demonstrate that in all modeled sub-basins and scenarios for spring-run Chinook salmon, the carrying capacity of holding habitat exceeds that of redd (spawning) carrying capacity in reaches with potentially suitable habitat. In all cases, predicted holding capacity (males and females) was more than twice that of predicted redd capacity (females only). This result suggests that when adult female escapement to freshwater and survival during holding are high enough to produce female spawners in excess of the redd carrying capacity, it is the quantity of spawning habitat that likely limits production of juveniles in the upper Yuba River watershed.

In the SY sub-basin, redd capacity under Alternative Management Scenarios 1 and 2 is 7 and 16 times higher, respectively, than current conditions. In the MY sub-basin, predicted redd capacity under Alternative Management Scenarios 1 and 2 is 7 and 17 times higher. In each case, the predicted increases are attributable primarily to the increase in suitable holding and spawning habitat that would result from increased summer flow. In the NBB sub-basin, the predicted increases in redd capacity under Alternative Management Scenarios 1 and 2 are 7 and 14 times higher than current conditions, reflecting the difference between partial and full restoration of spawning habitat specified for each scenario.

In the NY sub-basin, estimated redd capacity and age-0 summer rearing capacity under current conditions are substantially greater than the MY and SY sub-basins, even when compared with predicted MY and SY carrying capacities under the alternative management scenarios. The NY sub-basin was predicted to support 29% and 66% more redds under current conditions than the MY and SY sub-basins, respectively, would support under Alternative Management Scenario 2. Predicted holding habitat capacity in the NY sub-basin exceeds the predicted holding capacity in the SY and MY under current conditions and Scenario 1. Only under Scenario 2 does predicted holding capacity in the MY and SY sub-basins equal or exceed the NY sub-basin.

Carrying capacity for the age-0 summer rearing life stage reflects the relative potential of each sub-basin to provide over-summering habitat and produce yearling spring-run Chinook salmon smolts. Predicted habitat for age-0 summer rearing in the NY sub-basin under current conditions was 1.5 times greater than that predicted in the SY under Scenario 2, 1.9 times greater than that predicted in the MY under Scenario 2, and 1.2 times greater than that predicted in the NBB sub- basin under both alternative management scenarios. The predicted NY rearing capacity would be even greater if not for the relatively low frequency of pools in the NY compared with the other sub-basins. In the SY, MY, and NBB sub-basins, age-0 summer rearing capacity increased markedly under the alternative flow scenarios compared with current conditions, due to an increased length of thermally suitable channel and greater area of channel inundated during the summer low-flow period. The relatively high age-0 summer juvenile carrying capacity predicted for the NBB sub-basin compared with the MY and SY sub-basins under Alternative Management Scenarios 1 and 2 was attributed to the significantly wider summer low-flow channel. Age-0 summer rearing capacity did not increase in the NBB sub-basin between Alternative Management Scenarios 1 and 2, since the only difference between scenarios was augmentation of spawning gravels.

Smolt production estimates The spring-run Chinook salmon POP module used reach-specific carrying capacity values for holding, spawning, and summer rearing in conjunction with biological input parameters and life stage-specific stock-production curves, to estimate equilibrium population size. At the moderate

February 2012 Stillwater Sciences ES-6 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed smolt-to-adult survival parameter values used, predicted adult escapement was sufficient to fully seed available habitat for most model runs. However, holding habitat was not fully seeded in the SY sub-basin under Alternative Management Scenario 1 or in the MY and NBB sub-basins under current conditions. In each sub-basin and each scenario, the predicted number of spawners was greater than redds, indicating that predicted adult escapement was sufficient to fully seed the available spawning habitat. This result, in turn, indicates that smolt production estimates represent the maximum production potential at the freshwater survival parameter values used.

The POP module results further indicate that, in nearly all model runs, emergent fry production from available spawning gravels was sufficient to fully seed the age-0 summer rearing habitat with individuals destined to become smolts. In contrast, age-0 summer rearing habitat was not fully seeded in the NBB sub-basin under current conditions or Alternative Management Scenario 1 due to the limited quantity of spawning gravels in these scenarios.

Under the alternative management scenarios, juvenile production from each sub-basin was predicted to increase substantially compared with current conditions. This increased production is a result of a greater amount of spawning and age-0 summer habitat available. The POP module output also provides an estimate of the proportion of each juvenile life history type produced in each sub-basin and scenario. The proportion of each juvenile life history type (efry, smolt0 and smolt1) is important to the dynamics and viability of each population due the expected increased survival in the San Francisco Bay-Delta and the ocean with increasing size and age. The relative contribution of efry to juvenile production is similar between all scenarios, varying between 69% and 75% of the juvenile production. The fraction of the smolt0 population varied from 0% in the NBB sub-basin to 30% in the MY sub-basin under current conditions. The fraction of smolt1 varied between 2% in the MY sub-basin under current conditions and 25% in the NBB sub-basin.

The adult escapement estimates generated by the RIPPLE model provide only a rough estimate of the number of adults that likely return to each sub-basin under equilibrium population conditions. However, preliminary model gaming suggests that there would be sufficient adult escapement to fully seed the available spawning habitat at much lower smolt-to-adult survival values; thus we assumed that the number of adults predicted would not affect our smolt and juvenile production estimates. Notwithstanding these considerations, the primary objective of the model was to predict freshwater habitat capacity of holders, spawners, and juveniles and to estimate production of juveniles and smolts. The model results and discussion will serve as data inputs to a statistical model downstream of Englebright Dam to characterize Delta and ocean conditions.

Under current conditions, unsuitably high water temperatures would limit access by reintroduced spring-run Chinook salmon to over 30 miles of otherwise high quality mainstem spawning and rearing habitats in the SY and MY sub-basins, greatly limiting potential smolt production. Similarly, high water temperatures in the NBB sub-basin would restrict spawning and juvenile rearing to a fraction of otherwise suitable habitat, and lack of spawning gravel in thermally suitable reaches would further limit juvenile production. Nonetheless, model results indicate that in the North Yuba River under current conditions and the SY, MY, and NBB sub-basins under the alternative management scenarios, sufficient spring-run Chinook salmon holding, spawning, and rearing habitat exists to allow for production of substantial numbers of juveniles and smolts.

February 2012 Stillwater Sciences ES-7 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Steelhead Results Predicted distribution of suitable habitat In the SY sub-basin, under current conditions, suitable steelhead spawning and summer rearing habitat would include 0.3 miles of the mainstem and 15.9 miles of tributary habitat. Compared with current conditions, an additional 10.7 miles of the mainstem South Yuba River were predicted to be suitable for steelhead spawning and summer rearing under Alternative Management Scenario 1, while an additional 22.5 miles were suitable under Alternative Management Scenario 2. Suitable tributary habitat predicted under the alternative management scenarios was the same as under current conditions.

In the MY sub-basin, under current conditions 7.5 miles of the mainstem and 11.5 miles of tributary habitat were identified as suitable habitat for steelhead spawning and summer rearing. Compared with current conditions, an additional 6.7 miles of the mainstem were predicted to be suitable under Alternative Management Scenario 1, and an additional 18.4 miles under Alternative Management Scenario 2.

In the NY sub-basin, under current conditions, 34.7 miles of the mainstem and 43.5 miles of tributary habitat—considerably more than the SY and MY sub-basins—were identified as suitable habitat for steelhead spawning and summer rearing. Alternative management scenarios were not modeled in the NY sub-basin.

In the NBB sub-basin, under current conditions, 3.7 miles of the mainstem North Yuba River was identified as suitable summer rearing habitat for steelhead. However, due to lack of suitable spawning gravel in the mainstem between New Bullards Bar Dam and the Middle Yuba River confluence, spawning under current conditions was only predicted to occur downstream of New Colgate Powerhouse and in the lower 0.6 miles of Dobbins Creek. Suitable winter rearing habitat in the NBB sub-basin was assumed to be present under all scenarios in the entire mainstem channel and in lower Dobbins Creek. Under Alternative Management Scenarios 1 and 2, which stipulate increased cold water releases from New Bullards Bar Dam and spawning gravel augmentation, the entire 10.3 miles of mainstem channel from New Bullards Bar Dam downstream to Englebright Reservoir, and the lower-most 0.6 miles of Dobbins Creek, were predicted to be suitable for steelhead spawning and summer rearing.

Carrying capacity estimates Results of the RIPPLE HAB module indicate that, for each model sub-basin and scenario, there is sufficient steelhead spawning habitat (redd carrying capacity) to fully seed the thermally suitable age 1+ summer rearing habitat. Redd carrying capacity predicted for the NY sub-basin was substantially higher than the other sub-basins (regardless of scenario) due to a greater length and area of thermally suitable mainstem channel and the presence of extensive tributary habitat relative to other sub-basins.

Steelhead HAB module results also indicate that age 1+ summer habitat was considerably more limiting than winter habitat. Under current conditions, predicted age 1+ winter habitat capacity ranged from 30 to 512 times higher than summer rearing habitat capacity, depending on the modeled basin and scenario. These results indicate that the quantity of summer habitat will likely limit the potential size of the steelhead population in upper Yuba River watershed.

These pronounced summer rearing habitat limitations are, in part, attributable to the greater extent of thermally suitable channel in the winter than in the summer. Even in model runs where

February 2012 Stillwater Sciences ES-8 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed summer habitat was predicted to be thermally suitable in the entire mainstem study reach (NY sub-basin and NBB sub-basin under Alternative Management Scenarios 1 and 2), winter carrying capacity was still higher than summer carrying capacity due to the larger area of channel inundated during winter flows. Preliminary model gaming suggests that juvenile winter rearing density and/or the fraction of usable habitat would need to be reduced substantially before winter habitat becomes limiting.

Smolt production estimates Unlike spring-run Chinook salmon, the POP module was not fully parameterized or run for steelhead due to data limitations and the project scope of work. Potential steelhead smolt production in the upper Yuba River watershed was estimated based on carrying capacities predicted for age 1+ juveniles in the summer. Summer 1+ carrying capacity estimates from the HAB module were multiplied by summer and winter density-independent survival for each life stage to estimate smolt production.

For each model run, estimated smolt production mirrors summer 1+ carrying capacity predicted by the HAB module: significantly more smolts were produced under alternative management scenarios compared with current conditions. In the SY sub-basin, estimated steelhead smolt production under Alternative Management Scenarios 1 and 2 was 5 and 12 times higher, respectively, than current conditions. In the MY sub-basin, smolt production potential was about 2 and 4 times higher under Alternative Management Scenarios 1 and 2, respectively, than under current conditions. In the NBB sub-basin, estimated smolt production was 3.5 times higher under both alternative management scenarios compared with current conditions. These increases are driven in part by the increased length of mainstem channels that become thermally suitable and in part by the increased rearing area resulting from increased summer low-flow widths under the alternative management scenarios.

Estimates of smolt production further suggest that the NY sub-basin has the potential to produce substantially more steelhead than the SY and MY sub-basins, regardless of the scenario modeled. The NY sub-basin under current conditions was predicted to produce 1.5 and 2.1 times more smolts than the SY and MY sub-basins, respectively, even when the higher, less-restrictive water temperature criteria were applied under Alternative Management Scenario 2. As with age 1+ summer rearing carrying capacity, smolt production estimates generated from models run using the higher, less-restrictive water temperature criteria were substantially greater than estimates generated using the more conservative 20°C criterion. These results underscore the sensitivity of the model to the amount of suitable summer rearing habitat, as determined primarily by water temperature.

Several factors point to the upper Yuba River watershed, particularly the NY sub-basin, as having excellent potential for sustaining healthy steelhead populations. An abundance of high quality rearing habitat currently supports relatively high densities of resident rainbow trout in reaches with suitable summer water temperatures. Conditions for juvenile steelhead rearing in the upper Yuba River watershed are currently good, but as demonstrated by the model, alternative management to reduce summer water temperatures would greatly increase smolt production in the SY, MY, and NBB sub-basins.

February 2012 Stillwater Sciences ES-9 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Model Considerations: Sensitivity, Uncertainty, Challenges, and Validation Models serve as an invaluable tool to simulate and support the management of complex ecosystems. However, they are constrained by data availability, data quality, and the inherent simplification of a mathematical representation. Understanding potential model sensitivity and parameter uncertainty can stimulate improvements in model development and foster user confidence. As such, the evaluation of parameter uncertainty for spring-run Chinook salmon and steelhead models was focused on highly sensitive parameters, those likely to alter model results. Parameters with a low level of certainty and high level of sensitivity were recommended for additional evaluation. Key parameters for spring-run Chinook salmon included the proportion of efry and smolt-to-adult survival parameters. Key parameters for steelhead included age 1+ summer habitat capacity, the proportion of resident versus anadromous trout, and thermal suitability for additional tributary habitat. Additional studies of juvenile mortality due to predation were recommended for both species, along with studies to evaluate interspecies competition for steelhead.

Model challenges inherent to this study were documented for the sake of transparency. Model predictions and underlying assumptions that would benefit from future field validation efforts were also identified.

Model Application The RIPPLE model application for spring-run Chinook salmon and steelhead in the upper Yuba River watershed explored watershed-scale population dynamics, habitat capacity and productivity, species-specific limiting conditions and the relative benefits of various management alternatives. Each of these elements is an important when considering the reintroduction potential in the upper Yuba River watershed—the driving objective behind this study. Although there is always more work that can be done, this study incorporates the best available empirical information for each parameter and advances our knowledge of the upper watershed. As such, it serves as a key resource to support the reintroduction planning process.

February 2012 Stillwater Sciences ES-10 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed 1 INTRODUCTION

The lower Yuba River supports anadromous fish species including spring-run Chinook salmon (Oncorhynchus tshawytscha) in the California Central Valley Evolutionarily Significant Unit (ESU), steelhead (O. mykiss) in the California Central Valley Distinct Population Segment (DPS), and North American green sturgeon (Acipenser medirostris) in the Southern DPS. Currently, anadromous fish are restricted to the lower Yuba River because of a migration barrier presented by Englebright Dam as well as partial or complete barriers presented by DaGuerre Point Dam, New Bullards Bar Dam, Our House Dam, Log Cabin Dam, and associated hydropower facilities. In an effort to recover anadromous populations, the National Marine Fisheries Service (NMFS) is evaluating reintroduction potential above current barriers in the upper Yuba River watershed. As part of the Habitat Assessment and Reintroduction Implementation Plan for Central Valley spring-run Chinook salmon and steelhead, Stillwater Sciences was contracted to develop a spatially explicit model to quantify species-specific habitat carrying capacity and freshwater productivity potential upstream of Englebright Dam.

1.1 Goals and Objectives The primary goal of developing a quantitative model for spring-run Chinook salmon and steelhead in the upper Yuba River watershed was to assess the habitat capacity and productivity potential of these species under current and future conditions. To achieve the stated goal, the following objectives were set forth:  Identify suitable habitat for spring-run Chinook salmon and steelhead based on literature review, field assessments, modeling, consultations with NMFS staff and other scientists or knowledgeable experts, and professional judgment.  Simulate current carrying capacity and productivity potential for spring-run Chinook salmon in sub-basins of the upper Yuba River watershed.  Simulate current carrying capacity for steelhead in sub-basins of the upper Yuba River watershed.  In consultation with NMFS, model potential future conditions for salmon and steelhead resulting from flow, temperature, and habitat enhancements.  Identify reasonably recoverable habitats including stream reaches where managed flow regimes, supplemental flows, or other habitat restoration actions would provide satisfactory conditions for anadromous salmonids.  Collaborate with NMFS staff and regional stakeholders to ensure that all relevant information is incorporated into the assessment.

1.2 Approach To achieve the goals and objectives of this study, the following steps were implemented:  Review existing information pertinent to upper Yuba River sub-basin physical conditions and the ecology of Central Valley spring-run Chinook salmon and steelhead.  Characterize current physical conditions in the upper Yuba River sub-basins based on the best available science.  Develop a spatially explicit model (RIPPLE) to quantify habitat capacity and life cycle dynamics for spring-run Chinook salmon and steelhead.

February 2012 Stillwater Sciences 1 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

 Parameterize the model with data collected within the project area to the extent practicable.  Employ biological data from nearby watersheds if necessary and available for model parameterization. Data from northern California spring-run Chinook salmon and steelhead populations or other spring-run Chinook salmon and steelhead populations can be used in the absence of available local data.  Identify and apply limiting conditions that restrict habitat use (e.g., temperature constraints on spring-run Chinook salmon holding and rearing).  Minimize the confounding influence of downstream survival, by focusing the model simulations on freshwater conditions.  Simulate alternative flow, temperature, and habitat restoration scenarios.  Document data sources.  Document known model sensitivity and uncertainty.  Couple juvenile production potential generated by RIPPLE to a statistical model of downstream survival.

Compared with Chinook salmon, steelhead are inherently more challenging to model given their life history diversity and opportunistic behavior. As such, we modeled steelhead habitat capacity using simplified assumptions about steelhead life history and parameterized the steelhead model using readily available data. The potential effects of these model and parameter simplifications are discussed in this report along with recommendations for future model expansion, data collection, and parameter refinement.

In Section 8 of this report we discuss model challenges for both species of interest, along with opportunities for model validation and refinement. The value of additional information is linked to forthcoming management alternatives to be considered outside the scope of this study.

1.3 Basin Overview The upper Yuba River watershed extends from an elevation of 2,774 m (9,100 ft) at the crest of the Sierra Nevada to 161 m (527 ft) at Englebright Reservoir. Englebright Dam marks the division between the upper and lower Yuba River watersheds (Map 1). The majority of the upper Yuba River watershed is located in Sierra and Nevada counties. The upper Yuba River watershed consists of three major tributaries: the South Yuba River with a drainage area of 912 km2 (352 mi2), the Middle Yuba River with a drainage area of 543 km2 (210 mi2), and the North Yuba River with a drainage area of 1,266 km2 (489 mi2). The three major tributaries flow from east to west through steep, narrow mountain canyons. The area drained by each major tributary was treated as a separate sub-basin for RIPPLE modeling purposes. We also defined a fourth sub- basin for modeling purposes, consisting of the watershed area between New Bullards Bar Dam and Englebright Reservoir, which drains an area of 151 km2 (58 mi2). The upper North Yuba River is dammed by New Bullards Bar Dam to form New Bullards Bar Reservoir. Below New Bullards Bar Dam, the North Yuba River is joined by the Middle Yuba River, forming the Yuba River which flows into Englebright Reservoir. Farther downstream, the South Yuba River flows directly into Englebright Reservoir near the town of Bridgeport.

Englebright Dam, located on the Yuba River 23.4 river miles upstream of the Yuba River’s confluence with the Feather River, has no fish passage facilities and since its construction in 1941 has been a complete barrier to fish migration. New Bullards Bar Dam on the North Yuba River and Our House Dam on the Middle Yuba River are also complete barriers to fish passage. Prior to

February 2012 Stillwater Sciences 2 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed the construction of dams in the basin, the South Yuba, Middle Yuba, and North Yuba rivers are believed to have provided prime habitat for spring-run Chinook salmon and steelhead (Lindley et al. 2006; Yoshiyama et al. 1998, 2001). Both of these species currently occur in the lower Yuba River below Englebright Dam. NMFS (2002) considers the elimination of access to historical spawning and rearing habitat upstream of Englebright Dam to be the greatest impact to listed salmonids in the Yuba River watershed. In the 2009 Public Draft Recovery Plan for Central Valley salmon and steelhead, NMFS identified Englebright Dam as one of the dams where fish passage would contribute to recovery of the Central Valley spring-run Chinook salmon Evolutionarily Significant Unit (ESU) and the Central Valley steelhead Distinct Population Segment (DPS).

Flows in the South Yuba and Middle Yuba rivers are largely regulated by dams and associated water conveyance facilities, whereas the North Yuba River is unregulated upstream of New Bullards Bar Dam. River habitat conditions modeled by RIPPLE in the South Yuba and Middle Yuba rivers, and in the Yuba River and North Yuba River downstream of New Bullards Bar Dam, are defined in large part by flows released from the upstream dams. Spaulding Dam on the South Yuba River impounds Lake Spaulding, which receives water from the upper South Yuba River, Fordyce Creek, and Bowman Lake through the Bowman-Spaulding Canal. Releases from Spaulding Dam, together with releases from Bowman Dam on Canyon Creek, largely regulate flows in the South Yuba River downstream of these facilities. Jackson Meadows Dam and Milton Dam are the major water storage and diversion facilities in the headwaters of the Middle Yuba River, largely regulating flows in the Middle Yuba River downstream of Milton Dam. Our House Dam, located on the Middle Yuba River 12.5 miles upstream of its confluence with the North Yuba River, impounds water for diversion from the Middle Yuba River to Oregon Creek through the Lohman Ridge Tunnel. Tributaries of the South, Middle, and North Yuba rivers also influence flow conditions in the three major sub-basins.

Stream flows in the upper Yuba River are characterized by low and constant summer flows (generally mid-July through October), winter storm peaks, and spring snowmelt runoff (Figure 1- 1). Although the unregulated North Yuba River has greater flow peaks and a more pronounced spring runoff response than the South Yuba and Middle Yuba rivers, hydrographs for the three major tributaries in the upper Yuba River watershed indicate similar timing, duration, and frequency of runoff. For return intervals of 2–10 years, the three sub-basins also have similar peak flow magnitudes on a per unit drainage area basis (Stillwater Sciences 2010, unpubl. data).

February 2012 Stillwater Sciences 3 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

4,500 South Yuba (#11417500) Middle Yuba (#11408880) 4,000 North Yuba (#11413100)

3,500

3,000

2,500

2,000

1,500

1,000 Average daily discharge (cfs) for WY 1969-1987

500

0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Date Figure 1-1. Hydrographs for the South, Middle, and North Yuba rivers for the overlapping period of record (1969–1987). Source: USGS gage data.

The river channels in the upper Yuba River watershed are deeply incised, with alternating bedrock and alluvial reaches. Sediment in alluvial reaches is stored in the channel bed, active bars, and infrequent floodplains and terraces (Curtis et al. 2006). Beginning in the Gold Rush era, the upper Yuba River watershed was subject to intensive hydraulic mining, logging, water impoundment and diversion, and other anthropogenic disturbances. Hydraulic mining involved the use of high-pressure water to erode gold-bearing gravel deposits. The resulting sediment- laden runoff was processed for gold and conveyed directly into creeks and rivers, causing massive increases in sediment loads and extensive downstream channel aggradation (Mount 1995, Curtis et al. 2006). Currently land in the upper Yuba River watershed is predominantly in private and federal (mainly National Forest) ownership, with uses including timber harvest, recreation, grazing, and minor residential development.

The upper Yuba River watershed has a Mediterranean climate, with cool, wet winters and hot, dry summers. Approximately 85% of the annual precipitation occurs between November and April (Curtis et al. 2006), falling primarily as snow at the higher elevations and rain in the lower portion of the watershed. Vegetation in the watershed includes mixed conifer forest, pine and oak woodland, and chaparral. Native resident fishes in the upper Yuba River watershed include rainbow trout (Oncorhynchus mykiss), Sacramento sucker (Catostomus occidentalis), Sacramento pikeminnow (Ptychocheilus grandis), and hardhead (Mylopharodon conocephalus) (NID and PG&E 2009; Gast et al. 2005; Gard 2002, 2004). Non-native fishes present in the upper Yuba River watershed include brown trout (Salmo trutta), smallmouth bass (Micropterus dolomieu), and sunfish (Lepomis spp.) (Moyle and Gard 1993).

February 2012 Stillwater Sciences 4 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed 2 FOCAL SPECIES

2.1 Spring-run Chinook Salmon 2.1.1 Status and life history Spring-run Chinook salmon was at one time considered the most abundant salmon run in California’s Central Valley, with annual Sacramento River escapement estimated at approximately 600,000 spawners (Yoshiyama et al. 2001). Extensive habitat degradation from hydraulic mining and loss of habitat due to construction of water diversions and hydroelectric dams led to the collapse of most populations and the listing of the Central Valley spring-run Chinook salmon ESU as threatened under the Endangered Species Act (64 FR 50394). The ESU has been reduced from an estimated 17 historical populations to only three natural populations with viable spawning runs: Mill Creek, Deer Creek, and Butte Creek (Yoshiyama et al. 2001). Most suitable habitat in the historical range of the ESU is upstream of impassable dams (Yoshiyama et al. 2001, Moyle 2002). A small population of spring-run Chinook salmon occurs in the mainstem Yuba River below Englebright Dam. The Yuba River population appears to be small and heavily influenced by introgression from the Feather River hatchery and the fall-run population (Massa et al. 2010).

After spending 1–4 years feeding in the ocean, adult spring-run Chinook salmon in the Sacramento River basin begin their upstream migration in late January and early February (CDFG 1998a) and enter Sacramento River tributaries, primarily from April through June (Vogel 2006, Moyle 2002, Yoshiyama et al. 2001). Adults enter freshwater as sexually immature fish and hold in deep, cold pools for several months before spawning. Evidence indicates that holding adults become physiologically stressed at water temperatures greater than 19°C (Table 2-1). Spawning generally occurs between mid-August and October, peaking in September (Moyle 2002). Upon arrival at the spawning grounds, adult females dig shallow depressions called redds in suitably-sized gravels, typically in pool tails adjacent to cover and deeper areas. Water temperatures greater than 15.6°C are considered stressful for spawning adults (Table 2-1). The developing eggs remain in the redds until hatching, where water temperatures of less than 14.4° C are required for normal development (Table 2-1). Newly hatched alevin (yolk-sac fry) emerge from the substrate and complete absorption of the yolk sac prior to dispersal downstream to suitable rearing habitat.

Table 2-1. Water temperature criteria for spring-run Chinook salmon in the upper Yuba River watershed (source: Stillwater Sciences 2006a). Spring-run Temperature Primary Source(s) for Chinook time Chronic Notes temperature salmon life 1 2 period Optimal Suboptimal to acute information stage stress3 Bell (1986); Possible Hallock et al. blockage or (1970), Bumgarner Upstream <13.3°C 13.3–18.3°C >18.3°C delay of Apr–Jun et al. (1997), both migration (<56°F) (56–65°F) (>65°F) upstream as cited in migration at McCullough temps > 13.3°C (1999).

February 2012 Stillwater Sciences 5 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Spring-run Temperature Primary Source(s) for Chinook time Chronic Notes temperature salmon life 1 2 period Optimal Suboptimal to acute information stage stress3 Ward and Kier (1999): taken from Thermal criteria Berman (1990, as Adult mid Apr– <16°C 16–19°C >19°C are those used cited in USFWS holding late Sep (<60.8°F) (60.8–66.2°F) (>66.2°F) for Battle Creek 1996), Armour spring Chinook (1991), and CDFG (1998a), Ward et al. (2004, 2006) NOAA (2002, as <13.3°C 13.3–15.6°C >15.6°C cited in CDWR Spawning Sep–Oct (<56°F) (56–60°F) (>60°F) 2004), FERC (1993) Myrick and Cech (2001), Bell Egg late Sep– <12°C 12–14.4°C >14.4°C (1986), NOAA incubation Jan (<54°F) (54–58°F) (>58°F) (2002, as cited in CDWR 2004) Rich (1987), Fry & NOAA (2002, as juvenile <15.6°C 15.6–18.3°C >18.3°C entire year cited in CDWR rearing and (<60°F) (60–65°F) (>65°F) 2004), FERC outmigration (1993) 1 Feeding and growth occur; growth dependent on food availability. No sublethal or lethal effects. 2 No direct mortality, but may result in a higher probability of diminished success (i.e., sublethal effects), especially at high end of range. 3 Chronic exposure at the low end of the range results in sublethal effects, including reduced growth, reduced competitive ability, behavioral alterations, and increased susceptibility to disease. At higher temperatures in this zone, short-term exposure (minutes to days) results in death.

In the Sacramento River basin, fry generally emerge from the gravels between November and March (Fisher 1994, Ward and McReynolds 2001). Spring-run Chinook salmon typically spend one year or more rearing in fresh water before migrating to sea, but the length of time spent rearing in freshwater varies greatly depending on availability and thermal suitability of freshwater habitat (Lindley et al. 2004, Williams 2006). Juvenile spring-run Chinook salmon may disperse downstream as fry soon after emergence in the winter, early in their first spring or summer, in the late-fall as flows increase, or as yearlings after overwintering in fresh water (Healey 1991, Lindley et al. 2004). Although fry typically drift downstream following emergence (Healey 1991), movement upstream or into cooler tributaries following emergence has also been observed in some systems (Lindsay et al. 1986, Taylor and Larkin 1986). Juvenile Chinook salmon rearing densities vary widely according to habitat conditions, presence of competitors, and life history strategies (Lister and Genoe 1970, Everest and Chapman 1972, Bjornn 1978, Hillman et al. 1987, Reedy 1995).

Unlike rearing fall-run Chinook salmon, which are present in streams only in winter and spring when flows are generally highest and water temperatures lowest, juvenile spring-run Chinook salmon that remain in spawning streams through summer may be subject to conditions such as high water temperatures and reduced habitat availability resulting from warm weather and lower summer flows. Although rearing juvenile spring-run Chinook salmon can survive for short

February 2012 Stillwater Sciences 6 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed periods in water temperatures up to 25°C (Hanson 1991, Myrick and Cech 2001), they become physiologically stressed at temperatures above 18.3°C (Table 2-1). Nicholas and Hankin (1989) suggested that the duration of freshwater rearing is tied to water temperature, with juveniles remaining longer in rivers with cool water temperatures, such as the North Umpqua River, Oregon and most individuals outmigrating as fry in warmer streams such as Butte Creek, California. Under current conditions in the upper Yuba River watershed, particularly the South and Middle Yuba rivers, an “ocean-type” life history pattern would likely predominate, with most juveniles emigrating prior to the onset of excessively high summer water temperatures. In the North Yuba River, where a longer reach of the channel is thermally suitable for summer rearing, a greater fraction of the juvenile population may follow a “stream-type” life history pattern and emigrate as yearlings.

2.1.2 Conceptual model of key limiting factors By migrating upstream during the high stream flows of the spring snowmelt, spring-run Chinook salmon historically were able to access higher elevation reaches than fall-run Chinook salmon. Cold water in these upper reaches allowed them to hold through the summer prior to spawning when temperatures cooled in the fall. Spring-run adults hold throughout the summer in deep pools with cover, which helps to keep water temperatures low.

There are considerable costs associated with this life history as compared with the fall run, including 3–4 months’ less ocean growth, energy that would otherwise be dedicated to eggs going to fat reserves to allow oversummer holding without feeding, and high predation risk while oversummering. In contrast, the prime advantage of this spring-run strategy may be the ability to reach upstream spawning and rearing habitat that is inaccessible to the fall run, which resulted in spatial segregation of the runs on the spawning grounds and thus reduced competition for spawning and rearing habitat.

Spawning and rearing habitats that may be accessible to spring-run Chinook salmon, but inaccessible to fall-run Chinook salmon, include (1) areas above falls or obstacles that cannot be negotiated during the low flows of summer and fall, and (2) areas above reaches that become too hot for salmon in the summer and fall. During the high spring snowmelt flows, spring-run Chinook salmon can ascend many obstacles that are barriers to upstream migration at lower flows, and they can traverse reaches in the spring that will be too warm in the fall for adult salmon. In addition, spring-run migrate upstream prior to attaining sexual maturity, which may confer greater swimming performance and make them better able to pass obstacles and ascend streams to higher elevations than fall-run females, which migrate in a ripe, gravid condition.

Under historical conditions, the spring and fall Chinook salmon runs were often geographically isolated in terms of where they spawned in the basin, which maintained their genetic integrity. Where the spring and fall runs now must share spawning grounds, such as the lower Yuba River, fall-run Chinook salmon may dominate because of their longer growth period in the ocean, slightly larger size, and less time spent holding in the stream prior to spawning. Any hybridization between the two runs has tended to be to the detriment of the spring-run life history.

The requirement for cool holding pools in the summer limits spring-run Chinook salmon to holding in larger mainstem channels, higher elevation streams, or spring-fed streams. The higher- elevation streams generally used by spring-run Chinook salmon for spawning are commonly steeper, confined channels with minimal floodplain habitat. Channels of this type are usually coarse-bedded, predominantly cobble and boulder, with spawning gravel typically occurring in small patches, such as near large boulders, bank outcrops, or in short, wider reaches. For this

February 2012 Stillwater Sciences 7 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed reason, spawning gravel is often expected to be more limiting than holding habitat and thus availability of spawning gravel can be a key factor limiting production of juvenile spring-run Chinook salmon.

By spawning in reaches that remain cool all summer, spring-run Chinook salmon allow the juvenile population access to the cool summer water temperatures necessary for extended juvenile residence. However, due to the high fecundity of the species, juvenile summer rearing habitat may be easily saturated by even a small number of successfully spawning adults. Fry in excess of carrying capacity are likely to disperse downstream, which results in relocation to reaches that are often too warm for summer rearing, and that require emigration in the spring and early summer after only a few months of rearing—much like juvenile fall-run Chinook salmon. Therefore, summer rearing habitat limitations may also play a key role in regulating spring-run Chinook salmon populations.

A considerable number of spring-run Chinook salmon juveniles that rear through the summer begin migrating to the ocean prior to the onset of winter and spring high flow periods (Lindley et al. 2004). Those that overwinter and emigrate in the spring may be faced with high velocity flows and require refuge habitat such as deep pools, interstitial spaces within boulder or cobble substrates, and low velocity areas along river margins (Swales et al. 1986, Healey 1991, Levings and Lauzier 1991). However, in river systems where winter habitat is abundant and its quality is not overly degraded, availability of winter habitat is not expected to limit population productivity of spring-run Chinook salmon in comparison with summer rearing habitat. This is because the amount of winter habitat is typically very large compared with summer habitat, the extent of which is restricted by high water temperatures.

2.2 Steelhead 2.2.1 Status and life history Steelhead is the term commonly used for the anadromous life history form of rainbow trout (Oncorhynchus mykiss). Prior to 1850, it is estimated that Central Valley steelhead runs were between 1 and 2 million annually (McEwan 2001). Steelhead populations have since declined dramatically. From data collected in 1998–2000, Good et al. (2005) estimated that about 3,600 female steelhead spawn naturally in the entire Central Valley. It is estimated that more than 80 percent of historical spawning habitat is now inaccessible to the species due to impassable dams (Lindley et al. 2006). A small population of steelhead occurs in the mainstem Yuba River below Englebright Dam. This population is part of the California Central Valley DPS, which is listed as threatened under the Endangered Species Act (76 FR 50447).

Steelhead exhibit highly variable life history patterns throughout their range, but are broadly categorized into winter and summer reproductive ecotypes. Winter steelhead, the most widespread reproductive ecotype, become sexually mature in the ocean, enter spawning streams in summer, fall, or winter, and spawn a few months later in winter or late spring (Meehan and Bjornn 1991, Behnke 1992). Only winter-run steelhead stocks are currently present in Central Valley streams (McEwan and Jackson 1996). Unlike Pacific salmon, adult steelhead may return to the ocean after spawning and return to freshwater to spawn in subsequent years.

Steelhead remain in the ocean for 1–4 years before entering fresh water and migrating into their natal streams to spawn. In the Sacramento River, adult winter steelhead migrate upstream during most months of the year, beginning in July, peaking in September, and continuing through February or March (Hallock 1987, McEwan 2001). During migration, adult steelhead experience

February 2012 Stillwater Sciences 8 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed physiological stress at water temperatures higher than 21°C (Table 2-2). Adults hold until flows are high enough in tributaries to enter for spawning (Moyle 2002). Steelhead adults typically spawn in small streams and tributaries where cool, well-oxygenated water is available year-round (McEwan 2001). Spawning occurs from December through April, peaking from January though March (Hallock 1987). During spawning and egg incubation, steelhead require water temperatures less than 12.8°C to ensure successful embryonic development (Table 2-2). Female steelhead construct redds in suitable gravels, often in pool tailouts and heads of riffles, or in isolated patches in cobble-bedded streams. Eggs hatch after a 20–100 day incubation period, depending on water temperature (Shapovalov and Taft 1954, Barnhart 1991). Newly-hatched steelhead alevins remain in the gravel for an additional 14–35 days while being nourished by their yolk sac (Barnhart 1991). Under optimal conditions, fry emerge from the substrate just before total yolk absorption.

Table 2-2. Water temperature criteria for steelhead in the upper Yuba River watershed (source: Stillwater Sciences 2006a). Temperature Primary Source(s) for Steelhead life time Chronic Notes temperature stage 1 2 period Optimal Suboptimal to acute information stress3 NMFS (2000), McEwan and Upstream <11.1°C 11.1–21°C >21°C Jackson (1996), migration/ Aug–Mar (<52°F) (52–70°F) (>70°F) Lantz (1971, as adult residence cited in Beschta et al. 1987) NMFS (2000), Temperatures McEwan and <11.1°C 11.1–12.8°C >12.8°C inferred from Spawning Jan–Apr Jackson (1996), (<52°F) (52–55°F) (>55°F) incubation FERC (1993), temps Bell (1986) NMFS (2000), McEwan and Egg Jan–early <11.1°C 11.1–12.8°C >12.8°C Jackson (1996), incubation Jun (<52°F) (52–55°F) (>55°F) FERC (1993), Bell (1986) Fry & juvenile <18.3°C 18.3–20°C >20°C NMFS (2000), rearing and Jan–Dec (<65°F) (65–68°F) (>68°F) FERC (1993) outmigration 1 Feeding and growth occur; growth dependent on food availability. No sublethal or lethal effects. 2 No direct mortality, but may result in a higher probability of diminished success (i.e., sublethal effects), especially at high end of range. 3 Chronic exposure at the low end of the range results in sublethal effects, including reduced growth, reduced competitive ability, behavioral alterations, and increased susceptibility to disease. At higher temperatures in this zone, short-term exposure (minutes to days) results in death.

Juveniles typically rear in fresh water for 2–4 years before emigrating to the ocean in April–June (Barnhart 1991). In the Sacramento River, steelhead generally emigrate as 2-year-olds during spring and early summer months (Hallock et al. 1961, McEwan 2001). Emigration appears to be more closely associated with size than age, with 6–8 in (152–203 mm) being the most common length for downstream migrants. Downstream migration in unregulated streams has been correlated with spring freshets (Reynolds et al. 1993). Rearing steelhead, like spring-run Chinook salmon, therefore experience low flow conditions during summer and must contend with factors

February 2012 Stillwater Sciences 9 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed such as increased water temperature and reduced habitat area during summer that may reduce the quantity and/or quality of fresh water rearing habitat. Juvenile steelhead generally require water temperatures lower than 20°C to avoid physiological stress (Table 2-1); however, some strains of O. mykiss have been shown to grow well at temperatures as high as 22°C and maintain weight at temperatures as high as 25°C (Myrick and Cech 2001). Prior acclimation to higher temperatures can also result in tolerance of higher temperatures than would otherwise be possible. Gast et al. (2005) observed resident O. mykiss occupying habitats with measured maximum daily average water temperatures in summer 2004 of 25.2°C and 23.2°C in the South Yuba and Middle Yuba rivers, respectively.

Although age 1+ smolts may compose a substantial portion of outmigrating steelhead, their survival is poor and they often contribute little to the numbers of returning adults (Shapovalov and Taft 1954, Kabel and German 1967). Survival of steelhead smolts tends to be much greater if outmigration occurs at age 2+ or 3+. Steelhead migrating downstream as juveniles may rear for one month to a year in the estuary before entering the ocean (Barnhart 1991), and the growth that takes place in estuaries may be very important for increasing the odds of marine survival (Smith 1990, Bond et al. 2008). Persistence of a steelhead population is therefore highly dependent on the quantity and quality of habitat for older age classes of juvenile fish (i.e., age 1+ and older). Because larger fish have greater requirements for space and other resources, however, habitat for age 1+ and older fish is usually more limited than for age 0+ fish.

2.2.2 Conceptual model of key limiting factors The relatively extended freshwater rearing of steelhead has important consequences for the species’ population dynamics. The maximum number of steelhead that a stream can support is limited by food and space through territorial behavior, and this territoriality is necessary to produce steelhead smolts that are large enough to have a reasonable chance of ocean survival. Because of this life history and freshwater habitat requirements, the number of fish that a reach of stream can support is typically small relative to the average fecundity of an adult female steelhead. Consequently, rather than being controlled by reproductive success, quantity and quality of physical habitat (either in the winter or summer) during the juvenile freshwater rearing stage is the factor that usually governs the number of steelhead smolts produced from a stream.

During the freshwater rearing stages of their life histories, the physical habitat requirements for different age classes of steelhead are relatively similar, except that as fish age and grow they require more space for foraging and cover (Bjornn and Reiser 1991). We postulate that age 0+ steelhead rearing habitat does not typically limit smolt production in either winter or summer. Age 0+ steelhead can use shallower habitats and finer substrates (e.g., gravels) than age 1+ steelhead, which, because of their larger size, need coarser cobble and boulder substrates for velocity cover while feeding and as escape cover from predators. Because age 0+ steelhead can generally utilize the habitats suitable for age 1+ steelhead, but age 1+ steelhead cannot use the shallower and/or finer substrate habitats suitable for age 0+ steelhead, it is unlikely that summer habitat will be in shorter supply for age 0+ than age 1+ steelhead. In the winter, habitat may often become unsuitable for age 1+ steelhead at lower levels of sedimentation than for age 0+ steelhead. At higher levels of embeddedness, substrate will become unsuitable for both summer and winter rearing, but it will often be more limiting in winter because refuge from entrainment during winter freshets typically occurs deeper within the substrate. There may be stream systems or reaches where all available habitat is suitable for both age 0+ and age 1+ steelhead, but even in these instances the density of age 0+ steelhead that the habitat will support will be higher than for the larger age 1+ steelhead simply due to allometric increases in territory size. In situations where summer habitat is suitable for both age classes, competition for space between age 0+ and age 1+

February 2012 Stillwater Sciences 10 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed steelhead may restrict the numbers of age 0+ steelhead that the habitat will effectively support. In general, a reach of stream would commonly support far fewer age 1+ than age 0+ steelhead in both summer and winter.

Summer juvenile carrying capacity is strongly influenced by instream flows, which influence overall rearing habitat area, the depth and volume of pool habitat, connectivity between habitat types, and water temperatures. Streamflow also dictates the quantity of drifting invertebrates that reach feeding steelhead, such that at higher summer flows steelhead can better maintain feeding rates that allow them to meet the metabolic demands of elevated summer water temperatures. In river systems with high summer water temperatures or low stream flows, availability of suitable summer rearing habitat can limit steelhead smolt production.

Overwintering steelhead may suffer elevated mortality when they are displaced by high winter flows. Refuge from flood events requires that steelhead access deeper interstitial spaces in the substrate or other cover to avoid turbulent, high velocity conditions. Because steelhead tend to spawn and rear in higher gradient stream reaches with more confined channels, they have less propensity than other salmonid species for using off-channel slackwater habitat in winter, and a greater propensity for using in-channel cover provided by cobble and boulder substrates. As such, interstitial spaces in cobble or boulder substrate are considered to be the key attribute defining winter habitat suitability for juvenile steelhead (Hartman 1965, Chapman and Bjornn 1969, Meyer and Griffith 1997). During winter, juvenile steelhead will often hide within the substrate (or other cover) during the day, emerging only at night. In colder regions, juvenile steelhead may remain concealed in the substrate all winter. In river systems where cobble and boulder substrates are highly embedded by fine sediments, winter habitat can be degraded and overwinter carrying capacity can limit smolt production.

3 RIPPLE MODEL OVERVIEW

RIPPLE is a powerful analytical tool that uses an ecological process-based approach to model the effects of historical, current, and potential future watershed conditions as they affect salmonid habitat and populations. The model is a collaborative product of the National Science Foundation- funded National Center for Earth Surface Dynamics (NCED) and Stillwater Sciences. In addition to comparing watershed conditions and fish populations across time and restoration scenarios, it can provide a systematic, reliable characterization of habitat “hot spots” for salmon productivity within a watershed.

RIPPLE can function at spatial scales from individual stream reaches to small watersheds to whole regions or landscapes. It was specifically developed for use in conditions where limited data exist, and relies on digital elevation data and empirical relationships to estimate reach- specific habitat throughout a channel network. The model uses population dynamics models to estimate spatially explicit populations for each salmonid life stage. By changing these relationships, or inserting data from reach-specific field observations in the model, it is possible to model changes in habitats and examine how a restoration program might affect overall productivity through improvements in carrying capacity and survival during one or more life stages. Variable marine survival and ocean harvest can also be incorporated to understand the impact of these factors on population dynamics.

RIPPLE is made up of three modules: (1) a physical module (“GEO”), (2) a habitat carrying capacity module (“HAB”), and (3) a population dynamics module (“POP”). The model is open-

February 2012 Stillwater Sciences 11 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed source and public domain, and a coho salmon life history version can be downloaded from the NCED website at http://www.nced.umn.edu/RIPPLE2.html. The application of the RIPPLE model for spring-run Chinook salmon and steelhead required modification and expansion to accommodate the additional life history complexities of these species. For example, the “spring- run Chinook version” of RIPPLE includes an adult holding life stage, whereas the coho salmon version does not. As a result, it is not possible to duplicate the upper Yuba River RIPPLE results for spring-run Chinook and steelhead using the publically available coho salmon version of the model. Although the RIPPLE model is not proprietary, it was not within the contract scope for this project to develop a graphical user interface for these new species. When user interfaces are developed, the models used in this report will also be made publically available.

One of the guiding principles the model is the assumption that physical processes and the resulting environment—specifically topography, geology, drainage area, channel gradient, and channel longitudinal profile—are relatively unchanging. This assumption permits construction a digital model of terrain features that establishes a physical “template” based on available data for topography and channel network characteristics. This physical template dictates the characteristics of habitats, which in turn can be used to predict reach-specific historical, current, and potential future salmon habitat and thus the potential distribution and abundance of salmon and life stages in different parts of the watershed.

RIPPLE includes a multi-stage stock-production model that links habitat conditions to population productivity attributable to specific stream reaches or watersheds. Conceptually, the model allows adult and juvenile salmon to migrate through the watershed in search of available habitat, which they occupy at densities specified by the user. Its main advantage is that it allows the user to project how changes over time in habitat quality and quantity will affect multiple generations of salmon in terms of overall population performance. The model allows the user to explore various outcomes by changing habitat abundance and quality.

Refer to the following link for additional detail on model structure and theory http://www.stillwatersci.com/resources/RIPPLE_overview.pdf

4 MODELED SUB-BASINS AND ALTERNATIVE MANAGEMENT SCENARIOS

4.1 Sub-basins The upper Yuba River watershed was divided into four separate sub-basins for RIPPLE modeling purposes (Map 1). The sub-basins each have distinct attributes and physical habitat conditions that require unique sets of model parameters. Summary characteristics of each sub-basin and the extent of modeled channel for each are shown in Table 4-1. Additional information on the natural fish passage barriers on the mainstem South Yuba, Middle Yuba, and North Yuba rivers is shown in Table 4-2. Physical attributes of each sub-basin, including hydrology and hydraulic geometry, are described in Section 5. Habitat attributes used to parameterize the RIPPLE HAB module to predict carrying capacity in each sub-basin are described for spring-run Chinook salmon in Section 6.1.1 and for steelhead in Section 7.2.1.

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Table 4-1. Characteristics of modeled sub-basins of the upper Yuba River watershed. Contributing Downstream Upstream Sub-basin Description area (km2) RMa RMa,b Confluence with mainstem South Yuba Yuba River upstream to 912 0 35.7 River (SY) the natural barrier and all suitable tributaries Confluence with mainstem Middle Yuba Yuba River upstream to 544 0 35.1 River (MY) the natural barrier and all suitable tributaries New Bullards Bar Dam North Yuba upstream to the natural 1,266 0 51 River (NY) barrier (Love’s Falls) and all suitable tributaries Yuba River Upper extent of below New Englebright Reservoir 151 32 41.8c Bullards Bar (Rice’s Crossing) upstream Dam (NBB) to New Bullards Bar Dam a River miles (RM) refer to the mainstem of each river in each sub-basin. For the SY and MY, river miles begin at the confluence with the mainstem. River miles for the NY begin at the confluence with the MY. River mile numbering used in this report may not match numbering reported by others. b Upstream river miles for the SY, MY, and NY represent the location of natural barriers to migration based on coordinates reported by Vogel (2006) and information in Yoshiyama et al. (2001). c River mile numbering for the Yuba River below New Bullards Bar Dam starts over at the confluence with the Middle Yuba River. The upstream RM for this sub-basin was calculated as the sum of the channel downstream of the Middle Yuba confluence (RM 32–39.6) and upstream of the Middle Yuba confluence (RM 0–2.2).

Table 4-2. Mainstem fish passage barriers in the upper Yuba River watershed. Approximate Information River Barrier description location source (RM)a low- & high-flow barrier (two Vogel 2006, South Yuba River waterfalls, 13 ft and 7.5 ft 35.7 Appendix C in high) UYRSPST (2007) Vogel 2006, Middle Yuba low- & high-flow barrier 35.1 Appendix C in River (large landslide, > 10 ft high) UYRSPST (2007) Yoshiyama et al. North Yuba River waterfall(s) (Loves Falls) 51.0 (2001) a River miles represent the location of natural barriers to migration based on coordinates reported by Vogel (2006) for the South and Middle Yuba rivers, and information in Yoshiyama et al. (2001) for the North Yuba River. River mile numbering used in this report may not match numbering reported by others.

Only a portion of the stream channel network in any sub-basin would be accessible to reintroduced spring-run Chinook salmon and steelhead and provide suitable habitat for these species. The extent of the channel network used to model habitat carrying capacity and production was therefore limited to accessible portions of the channel network known or predicted to provide potential habitat. For purposes of this assessment, it was assumed that

February 2012 Stillwater Sciences 13 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed passage by salmon and steelhead would be possible in the mainstem reaches of each sub-basin up to existing natural passage barriers (Table 4-2). Known passage barriers in tributaries (e.g., Pauley Creek, a tributary to the Downie River in the North Yuba sub-basin) similarly limited the extent of accessible habitat in each sub-basin.

Accessibility of stream channels and suitability of habitat is different for salmon and steelhead due to differences in the species’ habitat requirements, life history timing, and physiological capabilities (see Section 2). A primary determinant of habitat suitability for salmonids is water temperature. Habitat suitability is also dependent on physical characteristics such as channel width and depth during critical periods in the species’ freshwater life history. Extent of upstream passage into tributaries was determined through a combination of channel gradient and channel width thresholds, described in more detail in the sections that follow. The extent of the river channel network modeled in each sub-basin was restricted to correspond with potentially suitable habitat for freshwater life stages of spring-run Chinook salmon and steelhead. Because the amount of suitable habitat for each species varies as a function of flow and related environmental conditions such as water temperature, RIPPLE modeling was conducted for a range of potential conditions, or scenarios.

4.2 Modeling Scenarios In each sub-basin, RIPPLE modeling was conducted for current conditions to predict carrying capacity and population potential for both spring-run Chinook salmon and steelhead. Additionally, in the SY, MY, and NBB sub-basins, RIPPLE modeling was conducted for two alternative management scenarios that represent potential future conditions resulting from implementation of flow and habitat enhancements. Because the North Yuba River upstream of New Bullards Bar Reservoir is unregulated, alternative flow management is not possible and alternative scenarios were not considered for the NY sub-basin. The alternative management scenarios modeled in the SY, MY, and NBB sub-basins were developed by NMFS to approximate the increase in habitat that may be available for reintroduced salmon and steelhead in each sub-basin under each scenario.

Alternative management scenarios were developed based on the ability of water storage projects (Yuba River Development Project [YRDP] and the Yuba Bear/Drum Spaulding [YBDS] Project) to alter instream flow releases to improve habitat for anadromous salmonids. The primary life stages of concern were adult holding for spring-run Chinook salmon and juvenile rearing for both spring-run Chinook salmon and steelhead, due to the presence of these life stages in freshwater habitat during the hottest months of the summer. The Upper Yuba River Studies Program (UYRSP) investigated the potential for the upper Yuba River watershed to support anadromous salmonids and found that summer water temperatures could be sufficiently high to prevent or severely limit use of the Middle Yuba and South Yuba rivers by salmon and steelhead (UYRSPST 2007). The alternative management scenarios were therefore targeted toward reducing water temperatures in the critical summer months through additional instream flow releases below Project dams. In the NBB sub-basin, the alternative management scenarios also include augmenting spawning gravel, which is currently limited below New Bullards Bar Dam (Nikirk and Mesick 2006).

The alternative management scenarios for spring-run Chinook salmon identify the amount of habitat (i.e., stream length) that may be used for summer holding and rearing, not a specific flow regime. In any given year, the amount of suitable habitat will vary based primarily on water temperature (a function of flow and meteorology), but also the physical and metabolic condition

February 2012 Stillwater Sciences 14 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed of the fish. Therefore, the amount of suitable habitat specified for the alternative management scenarios could be realized through a combination of increased instream flow releases, cool and wet meteorological conditions, or exceptional biological condition of the fish. The alternative management scenarios attempt to bracket the range of suitable habitat that is reasonable to expect with implementation of future stream flow management strategies aimed at improving quality and extent of summer habitat (i.e., the “reasonably recoverable habitat”). By specifying the extent of additional habitat made suitable, the RIPPLE modeling scenarios allow future flexibility when simulating the potential effects on reintroduced spring-run Chinook salmon and steelhead from a range of meteorological and biological conditions.

The current conditions scenario modeled by RIPPLE represents the theoretical minimum extent of suitable habitat for spring-run Chinook salmon and steelhead in the MY, SY and NBB sub- basins given the minimal (~5 cfs) flow releases from Project reservoirs, combined with the warm and dry meteorological conditions that occurred during the analysis period (i.e., 2010; see Appendix A). Alternative Management Scenario 2 approaches a reasonable upper limit on the extent of habitat that could be usable under optimal conditions. All other reasonable combinations of scenarios are thought to lie between these two points, with Alternative Management Scenario 1 being a midway point that corresponds to previous estimates made in the Upper Yuba River Watershed Chinook Salmon and Steelhead Habitat Assessment (UYRSPST 2007).

The upstream and downstream extent of potential habitat under each modeled scenario was defined for modeling purposes by applying four criteria: (1) known natural barriers (Yoshiyama et al. (2001) and Vogel (2006) (2) channel gradient thresholds, (3) channel width thresholds, and (4) water temperature thresholds. The resulting extent of potential habitat in each sub-basin under each scenario is shown for spring-run Chinook salmon in Table 4-3 and for steelhead in Table 4- 4. The use of these thresholds in defining distribution in each modeled scenario is described below; the prediction of channel gradient and channel width is described in Section 5.

Table 4-3. Spring-run Chinook salmon habitat predicted under each modeling scenario in sub- basins of the upper Yuba River watershed. Approximate length of spring-run Chinook salmon holding and summer rearing habitat (mi)a Sub-basin Alternative Alternative Current conditions Scenario 1 Scenario 2 mainstem 0 7.0 15.3 SY tributaries 0 3.3 3.3 mainstem 2.3 11.9 22.5 MY tributaries 0 0 0 mainstem 27.7 n/a n/a NY tributaries 7.0 n/a n/a mainstem 3.2 10.3 10.3 NBB tributaries 0 0 0 a Estimated length only includes portions of the channel network with predicted habitat carrying capacity values > 0. Some portions of the channel network that were predicted to be thermally suitable have channel gradients too steep for holding and were therefore predicted to have zero carrying capacity.

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Table 4-4. Steelhead habitat predicted under each modeling scenario in sub-basins of the upper Yuba River watershed. Approximate length of steelhead spawning and summer rearing habitat (mi)a Sub-basin Alternative Alternative Current conditions Scenario 1 Scenario 2 mainstem 0.3 11.0 22.8 SY tributaries 15.9 15.9 15.9 mainstem 7.5 14.2 25.9 MY tributaries 11.5 11.5 11.5 mainstem 34.7 n/a n/a NY tributaries 43.5 n/a n/a mainstem 3.7b 10.3 10.3 NBB tributaries 0.6 0.6 0.6 a Estimated length only includes portions of the channel network with predicted habitat carrying capacity values > 0. Some portions of the channel network predicted to be thermally suitable have channel gradients too steep for holding and were therefore predicted to have zero carrying capacity. b Rearing habitat only; no suitable spawning gravel under current conditions.

4.2.1 Current conditions The current upstream extent of accessible habitat in the mainstem North Yuba, Middle Yuba, and South Yuba rivers is defined by existing natural fish passage barriers (Table 4-2). As discussed previously, all modeling scenarios, including current conditions, assumed that upstream and downstream passage would be provided up to these absolute barriers. The upstream extent of accessible habitat in the mainstem Yuba River below New Bullards Bar Dam is defined by the dam. These locations define the maximum potential upstream extent of mainstem river habitat for spring-run Chinook salmon and steelhead. The upstream extent of accessible and suitable habitat in the mainstems and tributaries to the North, Middle, and South Yuba rivers under current conditions was further refined by applying species-specific channel gradient and width thresholds to restrict the modeled extent of the channel network.

4.2.1.1 Spring-run Chinook salmon It was assumed that adult spring-run Chinook salmon migrating to holding areas in the spring and early summer could not pass any portion of the channel network with a gradient of 12% or greater, or with a sustained (> 300 m) gradient of 8% or greater (CDFG 2003). Channels with a summer low-flow width less than 8.5 m (28 ft) were assumed to be too narrow to provide holding pools with suitable depth (≥ 1.2–2.4 m [4–8 ft]; Grimes 1983, Airola and Marcotte 1985, as cited in Vogel 2006) or spawning habitat. This assumption was based on the channel dimensions in the upper portions of the North and South forks of Antelope Creek where holding spring-run Chinook salmon are commonly observed (C. Harvey Arrison, CDFG, Red Bluff, California, pers. comm., 21 June 2011). This channel width also corresponds with the upstream-most spawning location in Butte Creek (Quartz Bowl) (McReynolds et al. 2005, Stillwater Sciences 2007a). For modeling purposes it was assumed that rearing did not occur in reaches upstream of spawning. Thus, these channel gradient and width thresholds were used to restrict the upstream extent of potential habitat for all life stages of spring-run Chinook salmon in all sub-basins under all scenarios. The resulting effects on carrying capacity and production of each spring-run Chinook salmon life stage in the upper Yuba River watershed are described in Sections 6.1 and 6.2.

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The downstream extent of suitable spring-run Chinook salmon holding and rearing habitat under current conditions was defined by a maximum weekly average temperature (MWAT) water temperature suitability limit of ≤ 19°C1. In each sub-basin, the boundary of “thermal suitability” for holding was the location in each mainstem river where the moving 7-day average of the average daily water temperature was measured or predicted to exceed 19°C eight consecutive times. This “repeated exceedance” criterion was based on observations in Butte Creek (Ward et al. 2004, 2006), where substantial spring-run Chinook salmon pre-spawn mortality occurred in two years when the average daily water temperature exceeded 19°C for greater than 11 and 16 days, which equate to five and 10 consecutive exceedances of a moving 19°C 7-day average water temperature, respectively.

For RIPPLE modeling purposes we also used 19°C to define the extent of thermally suitable habitat for rearing juvenile spring-run Chinook salmon, likely resulting in an overestimate of juvenile rearing habitat. However, the use of a slightly higher water temperature threshold than recommended for juvenile rearing may help account for the effect of cold water refugia from groundwater or tributary inputs that may not be captured at the spatial and temporal scales typically used when measuring and modeling water temperature data. Such cold water refugia can allow successful rearing in reaches that would otherwise be deemed too warm.

The downstream extent of spring-run Chinook salmon spawning habitat was modeled to extend a fixed distance downstream from holding habitat. Based on evidence from the literature we assumed that spring-run Chinook salmon will move downstream up to 4.8 km (3 mi) from holding areas to spawning locations; though most post-holding movement will be upstream (Hockersmith et al. 1994, Vogel 2006).

In the South and Middle Yuba rivers, boundaries of thermal suitability were determined using modeled water temperature (Appendix B; NID and PG&E 2011). The YRDP and YBDS water temperature modeling relied on water temperatures measured during summer 2009 as model input data. Notably, 2009 was a year with relatively high air temperatures and low stream flows compared with long term averages (Appendix A). Although this suggests that the data represent a conservative estimate of suitable habitat (i.e., an underestimate), it may also be representative of a future climate in which warm meteorological conditions become more persistent. In the North Yuba River, the downstream extent of thermal suitability was determined using water temperature data collected by NMFS in summer 2010 (Appendix C). Because 2010 was a year with above average stream flow and slightly cooler than average air temperatures (Appendix A), the data likely result in an overestimate of thermally suitable habitat when compared to the SY and MY sub-basins. In the North Yuba River downstream of New Bullards Bar Dam and the Yuba River downstream of the Middle Yuba River confluence, the extent of thermal suitability for spring-run Chinook salmon holding, spawning, and rearing was estimated using available water temperature data collected at locations upstream and downstream of the Middle Yuba River confluence and upstream and downstream of the New Colgate Powerhouse in portions of the summers of 2008, 2009, and 2010 (YCWA 2009, 2010; NID 2008). Where the distance between data collection points was too large to provide useful spatial resolution in the water temperature

1 In evaluating feasibility of salmon and steelhead reintroduction into the upper Yuba River watershed, Stillwater Sciences (2006a) recommended a MWAT of 19°C as the upper limit to avoid “chronic to acute stress” for holding spring-run Chinook salmon, and an MWAT of 18.3°C for fry and juvenile rearing and outmigration. These criteria were based on a review of published and unpublished water temperature criteria for Chinook salmon in the Sacramento River basin.

February 2012 Stillwater Sciences 17 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed data, linear interpolation was used to estimate the location at which the 19°C summer water temperature threshold for spring-run Chinook salmon was likely exceeded.

Using criteria described above we estimated the amount of potential habitat for spring-run Chinook salmon holding and rearing in each sub-basin (Table 4-3). These estimates represent the initial extent of the modeled channel network for spring-run Chinook salmon, providing the template for physical habitat predictions performed in the GEO module (Section 5) and the basis for estimates of carrying capacity and production in the HAB and POP modules, respectively (Section 6).

4.2.1.2 Steelhead As described above, the upstream limit of habitat for salmon and steelhead in the mainstem South Yuba, Middle Yuba, and North Yuba rivers is defined by the natural passage barriers (Table 4-2). Similarly, the upstream extent of available habitat in tributaries in each sub-basin is limited by known passage barriers, in conjunction with channel gradient and width thresholds. To define the upstream extent of modeled steelhead habitat in tributaries in each sub-basin it was assumed that adult steelhead migrating to spawning areas in the winter and spring could not pass any portion of the channel network with a gradient of 20% or greater, or with a sustained (> 300 m [984 ft]) gradient of 8% or greater (CDFG 2003). Channels with a winter baseflow width less than 2 m (6.6 ft) were assumed to be too narrow to provide suitable steelhead spawning habitat. This minimum spawning width threshold was based on professional judgment and unpublished observations. For modeling purposes it was assumed that rearing did not occur in reaches upstream of spawning. Thus, these channel gradient and width thresholds were used to define the upstream extent of tributary habitat for all steelhead life stages in all sub-basins under all scenarios. The resulting effects on carrying capacity for each steelhead life stage in the upper Yuba River watershed are described in Sections 7.1 and 7.2.

The downstream extent of potential steelhead rearing habitat under current conditions was defined by a water temperature suitability limit of ≤ 20°C MWAT2, which provides a conservative estimate of steelhead rearing distribution. In each sub-basin, the downstream boundary of thermal suitability for rearing was the location in each mainstem river where the MWAT was measured or predicted to exceed 20°C. Where the distance between data collection points was too large to provide useful spatial resolution in the water temperature data, linear interpolation was used to estimate the location at which the 20°C MWAT water temperature threshold was likely exceeded.

For modeling purposes it was assumed that all tributaries are thermally suitable for steelhead rearing. Although water temperature data were not available for all tributaries, evaluations of available tributary water temperature data for the SY, MY, and NY sub-basins suggests that the majority are thermally suitable, but that the lower reaches of some streams may become thermally unsuitable during hot months and years. The overall contribution of these short, potentially unsuitable lower tributary reaches to smolt production is expected to be minimal relative to the overall basinwide production. Furthermore, since the amount of thermally suitable habitat in tributaries does not change between scenarios, this potential overestimate does not affect comparisons among scenarios.

2 A 20°C MWAT is the low end of the range associated with chronic to acute stress for rearing steelhead in the Sacramento River basin, based on literature reviewed by Stillwater Sciences (2006a).

February 2012 Stillwater Sciences 18 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Water temperature data collected in the NY sub-basin by NMFS in summer 2010 (Appendix C) indicated that the MWAT in the upper mainstem North Yuba River upstream of New Bullards Bar Reservoir was below 20°C for the entire summer at all monitoring locations except the downstream-most site (“Below Canyon Creek,” RM 17), at which the MWAT of 20°C was reached on only three occasions. Based on these data, and considering the proximity of Slate Creek and Canyon Creek—both of which have generally suitable summer water temperatures for rearing steelhead (SFWPA 2007, Reedy 2009) and could be used by steelhead as cold water refuge habitat—we assumed for modeling purposes that the entire upper mainstem North Yuba River was potential habitat for rearing steelhead under current conditions (Table 4-4).

Water temperature data collected by YCWA and NID in the mainstem Yuba River, North Yuba River, and tributaries downstream of New Bullards Bar Dam indicate that summer water temperatures under current conditions are likely suitable for steelhead rearing (MWAT ≤ 20°C) in the reach between New Bullards Bar Dam and North Yuba RM 0.6 (just upstream from the Middle Yuba River confluence), downstream of New Colgate Powerhouse, and in a small amount of tributary habitat (YCWA 2009, 2010; NID 2008). For modeling purposes it was therefore assumed that potential steelhead rearing habitat in the NBB sub-basin under current conditions is limited to these two mainstem reaches and the small amount of tributary habitat. The extent of potential steelhead rearing habitat in tributaries in the NY and NBB sub-basins was defined by channel gradient and width thresholds (as described above), and water temperature data where available.

The downstream extent of potential spawning habitat in the SY, MY, and NY sub-basins under current conditions was assumed to be the same as the downstream extent of rearing habitat. This is based on the assumption that successful rearing depends on the availability of (thermally) suitable rearing habitat located downstream of spawning locations. Although steelhead spawning and incubation would presumably take place from January to early June when water temperatures in most parts of the upper Yuba River watershed are typically suitable (≤ 12.8°C MWAT)3, juveniles produced from redds in reaches where summer water temperatures are too warm for rearing would have a low likelihood of survival. For modeling purposes we also assumed that rearing only occurs downstream of spawning.

In the NBB sub-basin, potential spawning habitat in the mainstem Yuba River under current conditions was assumed to be present only downstream of New Colgate Powerhouse. Although the modeled extent of potential rearing habitat under current conditions includes the mainstem North Yuba River from North Yuba RM 0.6 to New Bullards Bar Dam, Nikirk and Mesick (2006) reported that no suitable spawning gravel currently exists in this reach.

Based on the extent of resident O. mykiss distribution observed by Gast et al. (2005) and the application of the criteria described above, we estimated the amount of potential habitat for steelhead spawning and summer rearing in each sub-basin (Table 4-4). These estimates represent the initial extent of the modeled channel network for steelhead, providing the template for physical habitat predictions performed in the GEO module (Section 5) and the basis for estimates of carrying capacity and smolt production (Section 7).

3 A 12.8°C MWAT is the low end of the range associated with chronic to acute stress for steelhead egg incubation in the Sacramento River basin (Stillwater Sciences 2006a). The use of this criterion for spawning is based on inference rather than evidence, due to a lack of available data.

February 2012 Stillwater Sciences 19 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

4.2.2 Alternative Management Scenario 1 Alternative Management Scenario 1 assumes that increased releases from dams in the SY, MY, and NBB sub-basins would increase the downstream extent of potential summer habitat for spring-run Chinook salmon and steelhead in these sub-basins compared with current conditions. Specific assumptions for each sub-basin and species are described below.

4.2.2.1 Spring-run Chinook salmon South Yuba sub-basin In the SY sub-basin, Alternative Management Scenario 1 assumes increased flow releases from Spaulding Dam on the South Yuba River and Bowman Dam on Canyon Creek would help provide suitable summer water temperatures to allow spring-run Chinook salmon holding and rearing in the mainstem South Yuba River from the natural fish passage barrier at RM 35.7 downstream to the confluence with Poorman Creek at RM 29. In Canyon Creek, summer water temperatures under Scenario 1 would be suitable for spring-run Chinook salmon holding and rearing from the natural gradient barrier at RM 3.3 downstream to the confluence with the South Yuba River. A total of 7 miles of mainstem habitat and 3.3 miles of tributary habitat (Canyon Creek) would potentially be available under this scenario (Table 4-3, Figure 4-1). For modeling purposes it was assumed that a passage solution would be provided to facilitate upstream and downstream fish passage past the small dam at the mouth of Canyon Creek. Other tributaries to the South Yuba River were not considered potential habitat for spring-run Chinook salmon due to channel gradient, channel width, water temperature, or a combination of these factors.

90

80

70 mainstem tributaries 60 (miles) 50 habitat 40

30 Holding 20

10

0 SY‐CC SY‐S1 SY‐S2 MY‐CC MY‐S1 MY‐S2 NY‐CC NBB‐CC NBB‐S1 NBB‐S2

Figure 4-1. Miles of stream thermally suitable for spring-run Chinook salmon holding in the mainstem and tributaries of each modeled sub-basin under current conditions and two modeled scenarios. Alternative management scenarios were not modeled for the North Yuba sub-basin. CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2.

February 2012 Stillwater Sciences 20 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Middle Yuba sub-basin In the MY sub-basin, Alternative Management Scenario 1 assumes increased summer flow releases from Jackson Meadows Reservoir through Milton Dam would provide thermally suitable spring-run Chinook salmon holding and rearing habitat downstream to RM 23.2 (between Wolf Creek and Kanaka Creek), a total of 11.9 mainstem river miles from the natural barrier at RM 35.1 (Table 4-3, Figure 4-1). Tributaries to the Middle Yuba River were not considered potential habitat for spring-run Chinook salmon due to channel gradient, channel width, water temperature, or a combination of these factors.

New Bullards Bar sub-basin In the NBB sub-basin, Alternative Management Scenario 1 assumes summer baseflow would be restored to unimpaired values in the mainstem North Yuba River from New Bullards Bar Dam to the Middle Yuba River confluence and the mainstem Yuba River from the Middle Yuba River confluence to Rice’s Crossing (the upstream extent of Englebright Reservoir assumed for modeling purposes), a total of 10.3 mainstem river miles (Table 4-3, Figure 4-1). Unimpaired summer baseflow in the NBB sub-basin was simulated in the model by applying the hydrologic geometry relationships developed for the unregulated NY sub-basin (Table 5-1 and Sections 5.2.1.1 and 5.2.2). The small tributaries in this sub-basin were not suitable for spring-run Chinook salmon due to channel gradient, channel width, water temperature, or a combination of these factors. Under this scenario it was assumed that water temperature would be suitable for all life stages of spring-run Chinook salmon at all times of year. Because of the large storage capacity and cold water pool of New Bullards Bar Reservoir, it was assumed the Yuba River Development Project (YRDP) could provide the necessary water to sufficiently cool the river down to Englebright Reservoir in every year.

Scenario 1 also assumes that a gravel augmentation program would be implemented to restore spawning habitat to approximately 50% of its unimpaired extent. The unimpaired extent (i.e., potential amount) of spawning gravel in the mainstem river in the NBB sub-basin was approximated based on the usable spawning habitat fraction calculated from the total spawning gravel area in the SY and MY sub-basins. It was assumed that the fraction of suitable spawning habitat in the SY and MY sub-basins provides a reasonable approximation of the spawning gravel that would be available in the mainstem river in the NBB sub-basin following gravel augmentation.

4.2.2.2 Steelhead South Yuba sub-basin In the SY sub-basin, increased summer flows under Alternative Management Scenario 1 would provide thermally suitable habitat for steelhead spawning and summer rearing in 11.0 miles of the mainstem South Yuba River (Table 4-4, Figure 4-2). This is an increase in 10.7 miles compared with current conditions. A “warming rate” (°C/river mile) was used to determine the downstream extent of suitable steelhead summer rearing in the mainstem. The downstream extent of spring- run Chinook salmon holding under Alternative Management Scenario 1 (Table 4-3 and Figure 4- 1) was used as a starting point. Based on the target MWAT for spring-run Chinook salmon holding of ≤ 19°C and the target MWAT for steelhead spawning and rearing of ≤ 20°C, the warming rate was used to determine the mainstem location downstream of the spring-run Chinook salmon holding extent where a 1°C increase in MWAT would occur. The warming rate for Alternative Management Scenario 1 was calculated using the HFAM water temperature model output on August 1, 2009 (the date on which the approximate annual daily maximum occurred) at

February 2012 Stillwater Sciences 21 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed upstream and downstream model nodes (Appendix B; NID and PG&E 2011). All of the 15.9 miles of potential tributary habitat under current conditions would remain under Scenario 1.

90

80

(miles) mainstem tributaries 70 habitat

60

50 spawning 40 and

30 rearing 20

10 Summer 0 SY‐CC SY‐S1 SY‐S2 MY‐CC MY‐S1 MY‐S2 NY‐CC NBB‐CC NBB‐S1 NBB‐S2 Figure 4-2. Miles of stream thermally suitable for steelhead summer rearing and spawning in the mainstem and tributaries of each modeled sub-basin under current conditions and two modeled scenarios. Alternative management scenarios were not modeled for the North Yuba sub-basin. CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2.

Middle Yuba sub-basin In the MY sub-basin, Alternative Management Scenario 1 would provide thermally suitable habitat for steelhead spawning and summer rearing in 14.2 miles of the mainstem Middle Yuba River, 6.7 miles more than under current conditions (Table 4-4, Figure 4-2). The warming rate approach described above for the SY sub-basin was also used in the MY sub-basin for Alternative Management Scenario 1. All of the 11.5 miles of potential tributary habitat under current conditions would remain under Scenario 1.

New Bullards Bar sub-basin In the NBB sub-basin, Alternative Management Scenario 1 would provide thermally suitable habitat for steelhead spawning and summer rearing in 10.3 miles of the mainstem and 0.6 miles of tributary habitat (Table 4-4, Figure 4-2). This represents an increase of 6.6 miles of mainstem habitat compared with current conditions.

As described above for spring-run Chinook salmon, Scenario 1 also assumes that a gravel augmentation program would be implemented to restore spawning habitat to approximately 50% of its unimpaired extent. This would result in suitable spawning habitat in the North Yuba River from New Bullards Bar Dam downstream to the Middle Yuba River confluence (this reach does not contain suitable spawning habitat under current conditions).

February 2012 Stillwater Sciences 22 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

4.2.3 Alternative Management Scenario 2 Alternative Management Scenario 2 assumes that dam releases in the SY, MY, and NBB sub- basins would be greater than those under Scenario 1 and would further increase the downstream extent of potential summer habitat for spring-run Chinook salmon and steelhead in these sub- basins compared with Alternative Management Scenario 1. Scenario 2 also assumes that a gravel augmentation program would be implemented to restore mainstem spawning habitat to its approximate unimpaired extent in the NBB sub-basin downstream of New Bullards Bar Dam. Specific assumptions for each sub-basin and species are described below.

4.2.3.1 Spring-run Chinook salmon South Yuba sub-basin In the SY sub-basin, Alternative Management Scenario 2 assumes increased summer flow releases from Spaulding Dam on the South Yuba River and Bowman Dam on Canyon Creek would provide a total of 15.3 miles of thermally suitable habitat for spring-run Chinook salmon holding and rearing in the mainstem South Yuba River. Thermally suitable habitat would extend downstream to the Humbug Creek confluence—an additional 8.3 miles of potential habitat compared with Scenario 1 (Table 4-3, Figure 4-1). Other than 3.3 miles of Canyon Creek below the natural gradient barrier, tributaries to the South Yuba River were not considered potential habitat for spring-run Chinook salmon due to the same factors described under Scenario 1.

Middle Yuba sub-basin In the MY sub-basin, Alternative Management Scenario 2 assumes increased summer flow releases from Jackson Meadows Reservoir through Milton Dam would provide a total of 22.5 miles of thermally suitable spring-run Chinook salmon holding and rearing habitat in the mainstem Middle Yuba River. Potential habitat would thus extend downstream to Our House Dam (RM 12.5)—an additional 10.6 miles of potential habitat compared with Scenario 1 and an additional 20.2 miles compared with current conditions (Table 4-3, Figure 4-1). Tributaries to the Middle Yuba River were not considered potential habitat for spring-run Chinook salmon due to the same factors described under Scenario 1.

New Bullards Bar sub-basin In the NBB sub-basin the extent of thermally suitable habitat for spring-run Chinook salmon under Alternative Management Scenario 2 would be identical to Alternative Management Scenario 1. Like Scenario 1, Scenario 2 assumes summer and winter baseflows would be restored to unimpaired values in the mainstem North Yuba River from New Bullards Bar Dam to the Middle Yuba River confluence and the mainstem Yuba River from the Middle Yuba River confluence to Rice’s Crossing (the upstream extent of Englebright Reservoir assumed for modeling purposes), a total of 10.3 mainstem river miles (Table 4-3, Figure 4-1). Scenario 2 likewise assumes that water temperature would be suitable for all life stages of spring-run Chinook salmon at all times of year.

Scenario 2 also assumes that a gravel augmentation program would be implemented to restore mainstem spawning habitat to its approximate unimpaired extent. Under Scenario 2 the fraction of spawning habitat (relative to total habitat area; i.e., the usable fraction) in the mainstem river from New Bullards Bar Dam downstream to Rice’s Crossing was assumed to be the same as in the mainstem South Yuba and Middle Yuba rivers. For modeling purposes we assumed that the fraction of suitable spawning habitat in the SY and MY sub-basins provides a reasonable approximation of the spawning gravel that would be available in the mainstem river in the NBB sub-basin following gravel augmentation.

February 2012 Stillwater Sciences 23 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

4.2.3.2 Steelhead South Yuba sub-basin In the SY sub-basin, increased summer flows under Alternative Management Scenario 2 would provide thermally suitable habitat for steelhead spawning and summer rearing in 22.8 miles of the mainstem river—an additional 11.8 miles of potential habitat compared with Scenario 1 and an additional 22.5 miles compared with current conditions (Table 4-4, Figure 4-2). The warming rate approach described for Alternative Management Scenario 1 was used to calculate the downstream extent of steelhead summer rearing. All of the 11.5 miles of potential tributary habitat under current conditions and Scenario 1 would remain under Scenario 2.

Middle Yuba sub-basin In the MY sub-basin, Alternative Management Scenario 2 assumes increased summer flow releases from Jackson Meadows Reservoir through Milton Dam would provide a total of approximately 25.9 miles of thermally suitable steelhead habitat in the mainstem Middle Yuba River—an additional 11.7 miles of potential habitat compared with Scenario 1 and an additional 18.4 miles compared with current conditions (Table 4-4, Figure 4-2). This increase is based on the warming rate approach described above. All of the 11.5 miles of potential tributary habitat predicted under current conditions and Scenario 1 would remain under Scenario 2.

New Bullards Bar sub-basin In the NBB sub-basin the extent of thermally suitable habitat for steelhead under Alternative Management Scenario 2 is identical to Alternative Management Scenario 1 (Table 4-4, Figure 4- 2). As described above for spring-run Chinook salmon, Scenario 2 assumes that a gravel augmentation program would be implemented to restore mainstem spawning habitat to its approximate unimpaired extent.

4.3 Expanded Steelhead Distribution The approach described above for defining suitable steelhead habitat is based on an assumed water temperature suitability criterion of ≤ 20°C MWAT for steelhead rearing. However, it is noteworthy that rainbow trout (O. mykiss) have been observed in the South and Middle Yuba rivers at relatively high densities considerably farther downstream than predicted based on this temperature criterion. It is possible that the use of a 20°C MWAT criterion results in a highly conservative estimate of steelhead habitat capacity, and that reintroduced steelhead could find suitable habitat where the MWAT is > 20°C. Indeed, 20°C is the recommended upper limit above which a decrease in fitness is likely; its use in predicting the spatial extent of steelhead distribution is expected to result in under-prediction. Therefore, to illustrate potential differences in steelhead habitat capacity and production that could result from the use of a single temperature criterion vs. observed rainbow trout distributions, a separate analysis was conducted and the results used to compare the two approaches.

The expanded steelhead habitat analysis was conducted only for the mainstem South Yuba and Middle Yuba rivers. In the NY sub-basin, the entire accessible channel network (mainstem and tributaries up to gradient or channel width threshold locations) was determined to be potentially suitable steelhead habitat using the 20°C MWAT criterion, so distribution could not be expanded. In the NBB sub-basin, the majority of the North Yuba River upstream of the Middle Yuba River confluence and the mainstem Yuba River downstream of New Colgate Powerhouse were determined to be suitable steelhead habitat using the 20°C MWAT criterion. An expanded

February 2012 Stillwater Sciences 24 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed steelhead habitat distribution in these areas would provide very little basis for comparison. In the mainstem Yuba River from the Middle Yuba River confluence downstream to New Colgate Powerhouse, the lack of reliable water temperature data, as well as the lack of reliable data on rainbow trout distribution or habitat suitability, precluded a reliable estimate of expanded habitat in this reach.

4.3.1 Current conditions The downstream extent of potential rearing habitat for steelhead in the mainstem South Yuba and Middle Yuba rivers under current conditions was determined based on observations of rainbow trout distribution during summer 2004 (Gast et al. 2005). Rainbow trout density in the South Yuba River was highest at snorkel survey sites upstream of RM 18.1, whereas density downstream of RM 18.1 was low and variable (Gast et al. 2005). In the Middle Yuba River, rainbow trout density was low and variable downstream of RM 17. Snorkeling and electrofishing surveys conducted in July and August 2008 (NID and PG&E 2009) corroborated the presence of rainbow trout in both the South and Middle Yuba rivers at least as far downstream as these locations. Based on the assumption that rainbow trout are a reasonable surrogate for steelhead, we used these locations in the mainstem South Yuba and Middle Yuba rivers to define an expanded downstream extent of potential steelhead rearing habitat modeled under current conditions. It should be noted that the observed presence of rainbow trout downstream of these expanded distribution limits, albeit at lower and more variable densities, suggests the possibility that reintroduced steelhead could use habitat even farther downstream than the expanded distribution. However, it is likely that fitness and reproductive success of steelhead in these lower reaches would be reduced due to increased susceptibility to disease, increased risk of predation, reduced dissolved oxygen, and other factors.

Under current conditions, 17.6 miles of the mainstem South Yuba River would be potentially suitable steelhead habitat using the observed location of rainbow trout to define the habitat extent (Table 4-5). This is an increase of 17.3 miles compared with the predicted amount of steelhead habitat using a 20°C temperature suitability criterion. In the Middle Yuba River, 17.9 miles of the mainstem would be potentially suitable for steelhead under current conditions using the observed location of rainbow trout to define the habitat extent (Table 4-5). This is an increase of 10.4 miles compared with the predicted amount of steelhead habitat using a 20°C temperature suitability criterion.

February 2012 Stillwater Sciences 25 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table 4-5. Comparison of steelhead habitat predicted in the mainstems of the South and Middle Yuba rivers using a ≤ 20°C MWAT criterion vs. higher water temperature criteria based on observed rainbow trout distribution.

Approximate length of steelhead spawning and summer Temperature rearing habitat (mi)a Sub-basin Criteria Alternative Alternative Current (MWAT) Management Management conditions Scenario 1 Scenario 2 20°Cb 0.3 11.0 22.8 SY 25.2°Cc 17.6 35.7 35.7 20°Cb 7.5 14.2 25.9 MY 23.2°Cc 17.9 23.4 35.1 a Estimated length only includes portions of the channel network with predicted habitat carrying capacity values > 0. Some portions of the channel network within the thermally suitable channel network have channel gradients too steep for holding and were therefore predicted to have zero carrying capacity. b Determined assuming 20°C MWAT thermal suitability criteria (SWS 2006) c Determined based on observations of rainbow trout by Gast et al. (2005) in summer 2004 and associated maximum daily average water temperatures.

4.3.2 Alternative Management Scenarios 1 and 2 For each alternative management scenario we estimated the downstream extent of expanded steelhead habitat based on the maximum daily average water temperatures recorded (by UYRSP temperature loggers) closest to the locations in the South Yuba River and Middle Yuba River where observed rainbow trout densities began to decline (i.e., RM 18.1in the South Yuba and RM 17 in the Middle Yuba; Gast et al. 2005). A warming rate was calculated, as described above in Section 4.2.2.2, to interpolate between temperature logger locations. This resulted in water temperature criteria of 25.2°C (MWAT) for the South Yuba River, and 23.2°C (MWAT) for the Middle Yuba River, which were used to determine the extent of suitable steelhead habitat in each mainstem river.

Under Alternative Management Scenario 1, the entire mainstem South Yuba River would be potentially suitable steelhead habitat (35.7 miles) using the observed location of rainbow trout to define the habitat extent (Table 4-5). This is an increase of 24.7 miles compared with the predicted amount of steelhead habitat using a 20°C temperature suitability criterion. In the Middle Yuba River, 23.4 miles of the mainstem would be potentially suitable for steelhead under Alternative Management Scenario 1 using the observed location of rainbow trout to define the habitat extent (Table 4-5). This is an increase of 9.2 miles compared with the predicted amount of steelhead habitat using a 20°C temperature suitability criterion.

Under Alternative Management Scenario 2, like Alternative Management Scenario 1, the entire mainstem South Yuba River would be potentially suitable steelhead habitat (35.7 miles) using the observed location of rainbow trout to define the habitat extent (Table 4-5). This is an increase of 12.9 miles compared with the predicted amount of steelhead habitat using a 20°C temperature suitability criterion. In the Middle Yuba River, the entire mainstem (35.1 miles) would be potentially suitable for steelhead under Alternative Management Scenario 2 using the observed location of rainbow trout to define the habitat extent (Table 4-5). This is an increase of 9.2 miles compared with the predicted amount of steelhead habitat using a 20°C temperature suitability criterion.

February 2012 Stillwater Sciences 26 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

5 STREAM CHANNEL NETWORK AND HYDRAULIC GEOMETRY

The GEO module, the first of three RIPPLE modules, stratifies the channel network based on fluvial geomorphology and is the physical template on which all subsequent modeling of aquatic habitat and population dynamics are performed. GEO inputs include digital elevation data, stream channel network, and hydraulic geometry relationships. The quality and resolution of these input data affect all subsequent model estimates. GEO implementation assumes that topography, the channel network, and hydraulic geometry do not change during the time scale over which biological responses are modeled (e.g., centuries).

Physical parameters utilized and predicted by the GEO model include the following:  Channel elevation and planform,  Channel order using both Strahler and Shreve systems;  Contributing drainage area at arc endpoints in the channel network;  Channel gradient;  Channel width and depth at bankfull flow, summer low flow, and winter base flow; and

 Median grain size (D50).

5.1 Stream Channel Network Development and Attribution Physical channel attributes such as gradient and contributing drainage area directly influence model predictions of the quantity and spatial distribution of aquatic habitat, and successful model implementation therefore requires an accurate, robust channel network. The channel network and related attributes in the upper Yuba River basin were developed using a National Hydrography Dataset (NHD) 1:24,000 vector channel network and a 1/3 arc second National Elevation Dataset (NED) DEM (digital elevation model) from which 10-m elevation contours were interpolated.

Drainage area was calculated by obtaining the contributing area to 10-m grid-cells and overlaying arc endpoints and tributary junctions. Drainage area calculations were done using the hydrological functions in ESRI’s ARCINFO, which fills artificial sinks in the DEM and allows flow to be routed along the path of steepest elevation drop in the terrain. Since this path in the DEM does not always follow the known channel alignment, known channels were “burned” into the DEM to force flow accumulation. Once the “burned” grid with the contributed areas was created, the endpoints and junctions of the arcs were used to extract the contributing area values from the cells they overlay. Map 2 shows the channel network in the upper Yuba River watershed stratified by contributing drainage area.

Channel gradient was calculated by intersecting the NHD channel network with 10-m elevation contours. Where a stream channel intersects a contour or tributary junction, nodes were created and attributed with an elevation value. Stream reaches were delimited using these contour intersections and tributary junctions. These reaches (also referred to as arcs) define the finest scale of RIPPLE analysis. Reach lengths are shorter in steep, incised terrain and longer in low- gradient areas (e.g., floodplains). Channel gradient in a reach was calculated as the elevation difference between reach endpoints divided by the length of the reach. Using exclusively vector channel data and the 10-m (33-ft) contours provided the best available data for calculating channel gradient in the project area and eliminated artifacts introduced by using a digital terrain model. Map 3 shows the Yuba River channel network stratified by channel gradient.

February 2012 Stillwater Sciences 27 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

5.2 Hydraulic Geometry Steam channel hydraulic geometry (width and depth) systematically increases in a watershed with increasing discharge according to the following power law functions (Leopold and Maddock 1953, Leopold et al. 1964): w = aQb d = cQf v = kQm where, w is width, d is depth, v is velocity, Q is discharge, and a, b, c, f, k, and m are coefficients.

Discharge also scales with drainage area according to a power law relationship, such that drainage area can be substituted for discharge. The substitution allows hydraulic geometry relationships to be developed where discharge data are sparse or unavailable.

The GEO module implements power law functions relating bankfull hydraulic geometry (width and depth) to drainage area at a site. Drainage area must be known at each bankfull measurement site in order to develop the power law relationship for bankfull hydraulic geometry. The GEO module implements linear functions relating hydraulic geometry at winter baseflow and summer low flow to the same hydraulic geometry variable at bankfull flow. Drainage area is not required to develop these linear relationships if width and depth measurements at bankfull flow, winter baseflow, and summer low flow are available.

Empirical hydraulic geometry relationships are typically developed from field measurements of channel width and depth acquired from sample sites stratified over the range of channel gradients and drainage areas in the watershed of interest. If data describing hydraulic geometry at bankfull flow, winter base flow, and/or summer low flow are incomplete or unavailable within the watershed of interest, channel geometry data acquired in nearby areas with similar characteristics governing fluvial processes (e.g., climate, bedrock geology, hillslope morphology, mass wasting processes, channel gradient and confinement) may be used to develop the relationships.

5.2.1 Current conditions in the upper Yuba River watershed Several data sources were available for developing hydraulic geometry relationships in the project area: 1. Flow and channel cross section data from USGS stream gaging sites in the NY, MY, and SY sub-basins; 2. Channel geometry (e.g., width and depth) measurements in the NY sub-basin (NMFS 2011, unpubl. data). 3. Channel cross sections surveyed in the MY and SY sub-basins (USGS, unpubl. data; Curtis et al. 2006);

Unique hydraulic geometry relationships were developed for different sub-basins to account for differences in unimpaired (NY sub-basin) and regulated (MY and SY sub-basins) hydrology and enable modeling of Alternative Flow Management scenarios in reaches with regulated hydrology (Table 5-1).

February 2012 Stillwater Sciences 28

+ 0.0073 + 0.0043 + 0.0043 + 0.0073 + bf bf bf bf

= 0.4744 D = 0.2010 D = 0.2010 D = 0.4744 D Stillwater Sciences lf lf lf lf Summer low flow Summer low - 1.4564 D + 0.0258 0.0258 + 0.0258 + D D bf sing. bf bf D 1 = 0.7694 W = 0.7694 = 0.3563 W = 0.3563 W = 0.3563 lf lf lf

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

Watershed Yuba River in the Upper ) W ) n/a -14 -14 - 0.0196 - 0.0196 W W + (6*10 + (6*10 + bf bf bf bf 29 = 0.6122W = 0.6122W Winter base flow flow base Winter = 0.8534W = 0.8534W wb wb wb wb W W W W 0.2939 0.2939 0.1518 0.1518 = 0.075 A = 0.075 A = 0.0066A = 0.0066A BF BF BF BF Hydraulic geometry relationships for the SY, MY, NY, and NBB sub-basins under current conditions. under sub-basins for the SY, MY, NY, and NBB geometry relationships Hydraulic D D D D 5-1. Bankfull flow Bankfull flow 0.4216 0.4216 0.400 0.400 Table

Width Depth Width Width Depth = 0.011 A = 0.011 A = 0.011 = 0.0077 A = 0.0077 A = 0.0077 bf bf bf bf

Technical Report Technical February 2012 Sub- basin Cros and Rice’s Dam Bar Bullards New between sub-reaches mainstem of three photographs aerial from were measured widths Sample 1 NY W MY W SY W NBB W Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

5.2.1.1 North Yuba sub-basin Hydraulic geometry relationships in the NY sub-basin under current conditions were developed from field measurements of channel widths and depths at 25 sites in the NY sub-basin (Appendix D and Appendix E). Surveys at each site included width and depth measurements of the bankfull channel and wetted channel during summer low flow (Appendix D, Table D-1). Relationships between drainage area and bankfull hydraulic geometry in the NY sub-basin are shown in Table 5-1 and Figure 5-1. Relationships between bankfull hydraulic geometry and summer low flow hydraulic geometry in the NY sub-basin are shown in Table 5-1 and Figure 5-2 and 5-3. Surveys did not include estimates of width or depth at winter baseflow. Winter baseflow width at the NY survey sites was therefore estimated by scaling the bankfull width by 0.85, the ratio of winter baseflow width and bankfull width at the NY gage site below Goodyear’s Bar (USGS gage # 11413000). Refer to Section 5.2.1.2 below for a description of how bankfull discharge, winter base flow, and summer low flow were determined at USGS gage sites. Relationships between bankfull width and winter baseflow width in the NY sub-basin are shown in Table 5-1 and Figure 5-2.

Bankfull Width Bankfull Depth y = 0.011x0.400 y = 0.075x0.1518 R2 = 0.90 R2 = 0.6002 100 10.0

10 1.0 Bankfull Depth, m Bankfull Width, m

1 0.1 1,000,000 10,000,000 100,000,000 1,000,000,000

2 Drainage Area, m Figure 5-1. Hydraulic geometry relationships for bankfull width and depth in the NY sub-basin.

February 2012 Stillwater Sciences 30 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Winter Baseflow Width Summer Low Flow Width y = 0.8534x + 6E-14 y = 0.7694x - 1.4564 R2 = 1 R2 = 0.9128 50

40

30

20 Flow Width,m

10 Winter Baseflow Width Summer or Low 0 0 1020304050

Bankfull Width, m Figure 5-2. Hydraulic geometry relationships for winter baseflow and summer low flow widths in the NY sub-basin.

Summer Low Flow Depth

y = 0.4744x + 0.0073 R2 = 0.6628 1.2

1.0

0.8

0.6

Summer FlowLow Depth,m 0.4

0.2 0.5 1.0 1.5 2.0 2.5

Bankfull Depth, m Figure 5-3. Hydraulic geometry relationship for summer low flow depths in the NY sub-basin.

February 2012 Stillwater Sciences 31 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

5.2.1.2 Middle Yuba and South Yuba sub-basins The approach to developing hydraulic geometry relationships in the MY and SY sub-basins involved (1) calculating model flow parameters (i.e., bankfull flow, winter baseflow, and summer baseflow) from long-term gage records, (2) extrapolating model flow parameters at gage sites to channel survey sites located throughout the two sub-basins, and (3) estimating channel widths and depths at model flows based on site-specific synthetic rating curves developed for channel survey sites. Model flow parameters were first calculated at USGS gages using peak and average daily discharge records over the period from water year 1969 to the most current date (Appendix D, Table D-2). Gage sites were selected based on their location with respect to impoundments and large tributaries and the period of record. Bankfull discharge at gage sites was approximated using the 1.5-yr return flow calculated from the annual peak discharge series; winter base flow was defined as the 90% exceedance flow for the period 1 January–30 April; and summer low flow was defined as the 90% exceedance flow for the water year.

Model flow values calculated at gage sites were extrapolated to 12 sites in the MY and SY sub- basins where the USGS surveyed channel geometry and modeled discharges (Appendix D, Table D-3) (Curtis et al. 2006; USGS unpubl. data). The 12 survey sites were selected from a larger number of USGS survey sites based on their representative drainage areas and quality of bankfull information collected in the field. Flow parameters were extrapolated to the 12 USGS survey sites using the flow transference method, which scales discharge from a gaged site to an ungaged site based on the ratio of drainage areas.

Channel widths and depths at the model flows were predicted at each of the 12 survey sites in the MY and SY using best fit power law regressions relating reported widths and depths to modeled discharges at a cross section within each site (USGS unpubl. data) (Appendix D, Table D-4). Bankfull hydraulic geometry relationships for the MY and SY sub-basins were then developed from best fit power law functions relating drainage area to estimated bankfull widths and depths at the 12 MY and SY sites, as well as seven small drainage area sites in the NY sub-basin surveyed by NMFS (Appendix D, Table D-1). Data from the NY sub-basin were included in the bankfull hydraulic geometry relationships for the MY and SY sub-basins because these NY sites have small drainage areas typical of unimpaired tributaries throughout the upper Yuba project area. Relationships between drainage area and bankfull hydraulic geometry in the MY and SY sub-basins are shown in Table 5-1 and Figure 5-4. Linear functions were developed to relate hydraulic geometry at winter baseflow and summer low flow to that at bankfull flow (Table 5-1 and Figures 5-5 and 5-6). Although RIPPLE predicts depths at winter baseflow, this variable was not used as input to the HAB module in the upper Yuba River watershed and is not discussed herein.

February 2012 Stillwater Sciences 32 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Bankfull Width Bankfull Depth 0.2939 y = 0.0077x0.4216 y = 0.0066x 2 R2 = 0.8581 R = 0.7904 100 10.00

10 1.00 Bankfull Depth, m Bankfull Width, m

1 0.10 1,000,000 10,000,000 100,000,000 1,000,000,000

2 Drainage Area, m Figure 5-4. Hydraulic geometry relationships for bankfull width and depth in the MY and SY sub-basins under current conditions.

Winter Baseflow Width Summer Low Flow Width y = 0.6122x - 0.0196 y = 0.3563x + 0.0258 R2 = 0.8944 R2 = 0.7216 40

35

30

25

20

15 Flow Width, m

10

5 Winter Baseflow WidthSummer or Low 0 0 102030405060

Bankfull Width, m Figure 5-5. Hydraulic geometry relationships for winter baseflow and summer low flow widths in the MY and SY sub-basins under current conditions.

February 2012 Stillwater Sciences 33 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Summer Low Flow Depth y = 0.201x + 0.0043 R2 = 0.4781 1.0

0.8

0.6

0.4 SummerFlow Low Depth,m

0.2 0.51.01.52.02.53.03.54.0

Bankfull Depth, m Figure 5-6. Hydraulic geometry relationship for summer low flow depths in the MY and SY sub- basins under current conditions.

5.2.1.3 Below New Bullards Bar Dam Hydraulic geometry relationships developed for the NY sub-basin under current conditions were used to predict width and depth in the NBB sub-basin under current conditions. To account for the effects of New Bullards Bar Reservoir and water diversions through New Colgate Power Tunnel on summer low flow width, summer low flow widths were measured in the mainstem North Yuba River and Yuba River channel downstream of New Bullards Bar Dam. Width measurements were sampled from National Agriculture Imagery Program (NAIP) aerial photography (23 June through 4 July 2009) at approximately 500 ft intervals in three mainstem sub-reaches between New Bullards Bar Dam and Rice’s Crossing. The mean width in each sub- reach was used as the summer low flow width in the sub-reach (Appendix D, Table D-5).

5.2.2 Alternative management scenarios Two alternative management scenarios were modeled to represent hypothetical increases in summer baseflow in the SY, MY, and NBB sub-basins, with the primary objective of increasing thermally suitable summer habitat for spring-run Chinook salmon and steelhead (see Section 4). In the NBB sub-basin, it was assumed that summer flows in the mainstem downstream of New Bullards Bar Dam under Alternative Management Scenarios 1 and 2 would be restored to unimpaired conditions, and that summer low-flow widths and depths under both scenarios would be accurately represent by hydraulic geometry relationships developed for the NY sub-basin under current conditions.

To model the potential benefits of Alternative Management Scenarios 1 and 2 on aquatic habitat in the mainstem Middle Yuba and South Yuba rivers using RIPPLE, unique hydraulic geometry

February 2012 Stillwater Sciences 34 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed relationships were developed for augmented summer low flows at the 12 USGS survey sites located in the MY and SY sub-basins (Appendix D, Table D-6). In the MY sub-basin, Alternative Management Scenarios 1 and 2 were assumed to represent increased summer releases from Milton Dam of 50 and 100 cfs, respectively. In the SY sub-basin, Alternative Management Scenario 1 was assumed to represent increased summer releases of 50 cfs from Spaulding Dam and 50 cfs from Bowman Dam, equating to an increase of 100 cfs in the South Yuba River downstream of Canyon Creek. Alternative Management Scenario 2 was assumed to represent increased summer releases of 100 cfs from Spaulding Dam and 100 cfs from Bowman Dam, equating to a total increase of 200 cfs in the South Yuba River downstream of Canyon Creek.

Summer low-flow widths and depths under the alternative management scenarios were predicted at each site using best fit power law regressions relating measured widths and depths to estimated discharges at each of the 12 USGS cross sections (Appendix D, Tables D-4 and D-6). Linear functions relating width and depth at summer low flow to bankfull width and depth were then developed for use in RIPPLE (Figures 5-7 and Figure 5-8), consistent with the methods described above for current conditions. Hydraulic geometry relationships were applied to specific reaches of the mainstem Middle Yuba River, South Yuba River, and Canyon Creek based on the hypothetical summer flow increases under each alternative management scenario (Appendix D, Table D-6).

Summer Low Flow Width (+ 50 cfs) y = 0.2861x + 4.55 R2 = 0.4933 Summer Low Flow Width (+100 cfs) y = 0.3144x + 5.2904 R2 = 0.5444 Summer Low Flow Width (+200 cfs) y = 0.3597x + 6.0763 R2 = 0.6222 40

30

20

10 Summer Flow Low Width, m

0 0 102030405060 Bankfull Width, m Figure 5-7. Hydraulic geometry relationships for summer low flow width in the MY and SY sub- basins under alternative management scenarios.

February 2012 Stillwater Sciences 35 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

y = 0.1848x + 0.2362 Summer Low Flow Depth (+50 cfs) R2 = 0.343 y = 0.1901x + 0.3481 Summer Low Flow Depth (+100 cfs) R2 = 0.3081

Summer Low Flow Depth (+200 cfs) y = 0.2056x + 0.4907 R2 = 0.2886 1.6

1.4

1.2

1.0

0.8

0.6 Summer Flow Low Depth, m 0.4

0.2 0.00.51.01.52.02.53.03.54.0 Bankfull Depth, m Figure 5-8. Hydraulic geometry relationships for summer low flow depth in the MY and SY sub- basins under alternative management scenarios.

Flows under the alternative management scenarios were assumed to be a constant increase above the current summer low flow, and the new relations are therefore parallel to trends in summer low flow observed under current conditions. The alternative management scenarios would not affect tributary flows (with the exception of Canyon Creek, a tributary to the South Yuba River), and the hydraulic geometry relations for summer low-flow width and depth under the alternative management scenarios were applied only to mainstem reaches of the South Yuba River, Canyon Creek, and Middle Yuba River downstream of the water storage reservoirs.

5.3 Application of GEO Module Results Channel widths predicted from hydraulic geometry relations in the GEO module are used for predicting wetted channel area, which is a key variable for predicting carrying capacity using the HAB module (Sections 6.1 and 7.1). Winter baseflow and summer low flow widths are particularly important in defining species distribution and for estimating carrying capacity. Under the alternative management scenarios, summer low flow widths increase in proportion to drainage area. The increase in summer low flow width under Alternative Management Scenario 2 would be substantially greater than under Alternative Management Scenario 1, with concomitant increases in available habitat per unit length of stream. These increases, as well as the increases in the downstream extent of suitable habitat under the alternative management scenarios, are reflected in the carrying capacity estimates generated by the HAB module (Sections 6.2 and 7.2).

February 2012 Stillwater Sciences 36 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

6 SPRING-RUN CHINOOK SALMON

6.1 Habitat Capacity (HAB) The primary goal of the HAB module is to calculate life stage-specific carrying capacities, or the maximum number of individuals of a given life stage that available habitat can support for the focal species. In the upper Yuba River watershed RIPPLE model, HAB was used to predict carrying capacity for adult holding habitat, redds, and age-0 summer rearing habitat. Juvenile winter carrying capacity was not modeled because it is not expected to limit smolt production. As described in Section 2.1.2, only a portion of over-summering juveniles are predicted to remain in the upper Yuba River watershed through the winter (Lindley et al. 2004). Additionally, winter habitat in the upper Yuba River watershed is abundant and of high quality (see Section 7.2.1.4 for more information on winter habitat quality), and more rearing habitat becomes available in the fall as water temperatures in the lower river reaches become cooler.

HAB uses the attributed channel network developed in the GEO module as a framework for defining habitat quality and quantity for each life stage. For example, channel width predicted for each reach by GEO is used to calculate habitat area, which is then used in conjunction with life stage-specific fish density values to calculate carrying capacity in that reach. GEO-predicted widths can also be used to restrict spawning and rearing to channels of a certain size. Alternatively, field data—if available—can be used in place of model-predicted values to parameterize the HAB module. Table 6-1 describes the HAB module input parameters used for the upper Yuba River RIPPLE model.

Table 6-1. Input parameters for the HAB module. HAB parameters Description Relative fractions of pool, riffle, run, and cascade Habitat type fraction habitat units (by channel length) in each channel gradient class in the study watershed. Maximum number of individuals per square meter Fish density for a given life stage, habitat type, and channel gradient class combination. Fraction of channel area in each habitat type and Usable fraction gradient class available for use by a specific life stage. Channel width and depth thresholds were assigned Channel width and to filter out portions of the stream network with depth thresholds predicted widths or depths less than or greater than those usable by a given life stage.

6.1.1 Methods 6.1.1.1 Channel gradient and habitat type composition The first step in applying HAB was to determine the channel gradient classes that equate to reaches with different morphology and, consequently, differing habitat quality and quantity for each life stage of the focal species. The gradient classes used for the upper Yuba River model application are: 0–1%, 1–2%, 2–4%, 4–8%, and 8–12%. These classes were used to stratify model parameters and model habitat for both spring-run Chinook salmon and steelhead not only

February 2012 Stillwater Sciences 37 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed because of geomorphic considerations but also because they included gradients significant to the spawning and rearing distributions and densities of both species. Gradients greater than 12% were not considered passable by spring-run Chinook salmon or steelhead and therefore were not included in the modeled channel network. For each channel gradient class, the HAB module requires life stage-specific data on habitat type composition, fish density, fraction of usable habitat, and suitable channel widths, depths, and substrate sizes. These data were derived from the best available sources with highest priority given to data from the study watershed, nearby watersheds or watersheds with similar geomorphology and hydrology and include published literature, unpublished reports, and unpublished field data.

Habitat typing data collected in the upper Yuba River basin were used to calculate habitat type fraction as parameters for each model sub-basin. For the SY and MY sub-basins, remotely derived and field-verified habitat typing data collected as part of the UYRSP rearing habitat assessment from approximately 69 km (43 mi) of the mainstem South Yuba River and 72 km (45 mi) of the mainstem Middle Yuba River (Stillwater Sciences 2006b) were used to parameterize habitat type fraction. For the NY sub-basin, habitat typing data collected by NMFS in fall 2010 were used to parameterize the HAB module (Appendix E). The NMFS data were collected specifically for this RIPPLE modeling application at 12 sites, each with 10–15 habitat units, across a range drainage areas and channel gradient classes in the NY sub-basin. For the NBB sub-basin, habitat typing data provided by HDR|DTA from field surveys of approximately 1.6 km (1 mi) upstream and downstream of Colgate Powerhouse were utilized (K. Peacock, HDR|DTA, Bellingham, Washington, pers. comm., 1 December 2010). The NBB data were not gradient class-specific, so we assigned equal fractions of each habitat type to each of the five gradient categories. Habitat type fraction values were assumed to be the same for all model scenarios. The habitat type fraction data are provided in Appendix F (Table F-1).

Life stage-specific density and usable fraction values were assigned for each channel gradient and habitat type combination (e.g., 0–1% pools) to calculate habitat carrying capacity for each life stage, as described in the following sections.

6.1.1.2 Holding density and usable fraction Spring-run Chinook salmon holding density values were parameterized based on examination of photographs of spring-run Chinook salmon holding at high density in Butte Creek, California. From these photographs, it was our professional judgment that spring-run Chinook salmon can hold at densities ranging from 0.5–1.5 fish/m2 (Stillwater Sciences 2003). For each of the upper Yuba RIPPLE model sub-basins and alternative management scenarios we selected the midpoint of this range (1.0 fish/m2) as the maximum density of holding adults (males and females) in pools in all gradient classes. We assumed zero holding in all other habitat types.

The amount of usable holding habitat, or usable fraction, was calculated by first determining the proportion of pools considered suitable for holding. This was achieved by comparing the number of suitable holding pools (Vogel 2006) to the total number of pools (Stillwater Sciences 2006b) located in the mainstem Middle Yuba and South Yuba rivers. The portion of each holding pool suitable for holding was then calculated by applying a scaling factor. This fraction likely varies depending on channel shape, hydraulics, water temperature and dissolved oxygen concentration of a given pool (C. Harvey Arrison, CDFG, Red Bluff, California, pers. comm., 21 June 2011). The suitable area of each holding pool was assumed to be, on average, 50% under current conditions and 75% under the two alternative management scenarios (Scenarios 1 and 2) based on professional judgment and observations of spring-run Chinook salmon holding at high densities in bedrock-controlled pools in Butte Creek. While increased flow (as under Scenarios 1 and 2)

February 2012 Stillwater Sciences 38 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed would likely provide only negligible increases in pool area4 compared with current conditions, it was assumed that increased flow would provide more substantial increases in pool depth, the extent of the bubble curtain and whitewater at the pool head, the length of the pool tail, and the concentration of dissolved oxygen. All of these factors could increase the amount of suitable holding habitat in each pool. Holding pool area was therefore multiplied by 0.5 (for current conditions) or 0.75 (for the two alternative management scenarios) to derive the total amount of holding habitat in the MY and SY sub-basins (Appendix F, Table F-2). No data on the number of holding pools were available for the NY or NBB sub-basins; therefore data from the SY and MY were stratified by gradient category and used to derive usable holding fraction parameters for the NY and NBB sub-basins (Appendix F, Table F-3). Additional detail on the methods and results of the usable fraction analysis for holding habitat are provided in Appendix F, Tables F-2 and F-3.

6.1.1.3 Spawning density and usable fraction Data on spring-run Chinook salmon spawning density and fraction of channel area usable for spawning were applied in the HAB module to predict carrying capacity, expressed as number of redds. Spawning density data from the upper Yuba River basin were not available; therefore spawning density was calculated based on the mean redd size measured in the McKenzie River, Oregon: 5.4m2 (Stillwater Sciences 2006c). Assuming one female per redd, this redd size equates to a spawning density of 0.185 females per m2. The redd size value of 5.4 m2 was comparable to the mean redd size reported for spring-run Chinook salmon in a variety of published and unpublished sources (Table 6-2).

Table 6-2. Mean sizes of spring-run Chinook salmon redds. Source Mean redd size (m2) Burner (1951)1 3.3 Cramer and Hammack (1952)2 4.0 Needham et al. (1943) 3.6 Neilson and Banford (1983)3 9.5 Reiser and White (1981)1 6.0 Mean 5.3 1 As cited in Bjornn and Reiser 1991 2 As cited in Moyle et al. 1995 3 As cited in Healey 1991

The usable fraction of spawning habitat was calculated for each gradient category and habitat type combination by dividing the area of suitable spawning gravel by the total channel area. Suitable spawning gravel area for Chinook salmon in the South and Middle Yuba rivers and the mainstem Yuba River downstream of New Bullards Bar Dam was calculated from spawning gravel data collected by (Nikirk and Mesick 2006)5. We assumed all gravel patches with median grain size less than 15 mm and greater than 80 mm were unsuitable for Chinook salmon spawning (Kondolf and Wolman 1993). The effects of superimposition on spawning habitat were accounted

4 Many of the large, deep pools in the upper Yuba River watershed are bedrock-controlled and steep-sided. Increased flows would therefore tend to increase pool depth but not width or length. 5 To account for the requirement of spring-run Chinook salmon to have nearby refuge habitat (defined as pools greater than 2.4 m [8 ft] deep or 1.2–2.4 m [4–8 ft] deep with cover) during spawning, suitable gravel area for each channel gradient class was reduced by 12% for the South Yuba and 20% for the Middle Yuba, following the methods used by Nikirk and Mesick (2006).

February 2012 Stillwater Sciences 39 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed for in the stock-production relationship applied from the spawner to egg life stages in the POP module. The estimated amount of spawning gravel area in 0–4% gradients was then apportioned among habitat types by assuming 80% of spawning gravel is in pools, 10% in riffles, 10% in runs, and 0% in cascades. This assumption was based on professional opinion and evidence from the literature that most spawning occurs in pool tails (Barnhart 1991, CDFG 1998a, b). We assumed spring-run Chinook salmon spawning did not occur in riffles or runs with gradients ≥ 4%. Total channel area for each gradient and habitat type class was calculated using GIS channel gradient data and the RIPPLE GEO module output for summer low flow width (Section 5). Since spawning habitat data were not available for the North Yuba, the usable fraction values calculated from combined South and Middle Yuba spawning habitat data were applied to the North Yuba. For the SY, MY, and NY model runs, the same spawning parameter values (i.e., density of spawners and usable fraction) were used for all scenarios. However, increased spawning carrying capacity is accounted for under the alternative management scenarios, since capacity is affected by the GEO-predicted channel area, which increases with increasing stream flow (Figure 5-9). Spawning density and usable fraction values used in the SY, MY, and NY model runs for each sub-basin are shown in Appendix F, Table F-4.

In the NBB sub-basin, the usable fraction of spawning habitat under current conditions was calculated as described above for the MY and SY. In their evaluation of spawning habitat, Nikirk and Mesick (2006) did not observe suitable spawning habitat in the NBB reach upstream of the Middle Yuba confluence. Therefore, in the Current Conditions model run, spawning capacity of this reach was set to zero. As described in Section 4, Alternative Management Scenarios 1 and 2 assume that gravel augmentation would occur in the Yuba River below New Bullards Bar dam, which was simulated in the NBB model run by increasing the usable fraction of spawning habitat for each habitat type. We assumed that the quantity of spawning gravels measured in the SY and MY represents a reasonable target for spawning habitat restoration and thus applied usable fraction values calculated for these sub-basins to NBB Scenario 2. As described in Section 4.2.3, Alternative Management Scenario 2 was developed by NMFS with the assumption that spawning gravel in the NBB sub-basin would be restored to its approximate unimpaired extent. Under Alternative Management Scenario 1, NMFS assumed that the amount of spawning gravel restored in the NBB sub-basin would be half the amount restored under Scenario 2. For modeling purposes, Scenario 1 values were thus calculated as 50% of each usable fraction value used in Scenario 2. Spawning density and usable fraction values used in the NBB model runs for each sub-basin are shown in Appendix F, Table F-5.

6.1.1.4 Juvenile rearing density and usable fraction Carrying capacity for over-summering juveniles was calculated in the HAB module from density and usable fraction parameters and channel area predicted by the GEO module (Section 5). Summer juvenile densities for each model run were parameterized using spring-run Chinook salmon juvenile densities estimated in July for low-gradient (0.5%) and higher gradient (1.3%) reaches of Johnson Creek, Idaho (Everest and Chapman 1972). Densities in the low-gradient reach averaged 1.8 fish/m2 (0.16 fish/ft2); whereas densities in the higher gradient reach averaged 0.5 fish/m2 (0.05 fish/ft2). These values were used to parameterize the HAB module for the 0–1% and 1–2% gradient classes, respectively (Appendix F, Table F-6).

The juvenile spring-run Chinook salmon summer density data reported by Everest and Chapman (1972) were collected from reaches containing a diversity of habitat types, but were not reported by habitat type. Therefore, juvenile densities from Johnson Creek were apportioned into each habitat type in proportion to habitat-specific (i.e., pool, riffle, and run) densities of juvenile spring-run Chinook salmon reported by Bjornn and Reiser (1991) for 22 Idaho streams (Table 6-

February 2012 Stillwater Sciences 40 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

3). The 2–4% and 4–8% gradient classes were parameterized with the same density values as the 1–2% gradient class, but usable fractions were lowered to 0.75 and 0.25, respectively, to reflect the lower carrying capacity expected at higher gradients (Appendix F, Table F-6). Higher gradient reaches have higher water velocities, thus reducing usability by juvenile Chinook salmon, especially those of smaller size (Everest and Chapman 1972). Juvenile rearing densities and usable fractions were not changed between model scenarios.

The Johnson Creek juvenile density data were selected for two reasons: (1) the data presumably represent fully-seeded, high quality summer rearing habitat in a river system containing both juvenile Chinook salmon and steelhead and with a summer base flow similar in magnitude to the North Yuba River (~150 cfs), and (2) we could not locate gradient-stratified summer juvenile density data for northern California spring-run Chinook salmon that could be considered to represent fully-seeded rearing habitat conditions in the upper Yuba River watershed. Numerous other sources of juvenile Chinook salmon rearing density data were evaluated for potential use in the model, including data from the Upper Sacramento River (CDFG 1998b) and Deer Creek (USFS 1992, unpubl. data). The Upper Sacramento River data were not used due to the large channel size and the fact that many fish were likely migrating at the time of sampling. Data from Deer Creek were not used since observed densities were low compared with many other sources we reviewed and likely did not represent a fully seeded system. The Johnson Creek juvenile spring-run Chinook salmon summer densities reported by Everest and Chapman (1972) are within the range of those from other river systems containing high quality summer habitat (Table 6-3).

Table 6-3. Summer rearing densities reported for age-0 spring-run Chinook salmon. Density (fish/m2) Data location Source Notes Pool Riffle Run Maximum values from snorkel Upper Sacramento CDFG (1998b) 1.250 1.100 1.650 surveys conducted between RM River, CA 271 and RM 302 USFS (1992, unpubl. Maximum values from snorkel Deer Creek, CA 0.570 0.139 0.313 data) surveys Mean of fall Chinook values Middle Fork Smith Reedy (1995) 0.111 0.005 0.018 from head, body, and tail of River, CA each habitat type Numerous Idaho Bjornn and Reiser Mean values of 22 streams 0.220 0.030 0.130 streams (1991) sampled in 1985 and 1986 Everest and Chapman Mean densities in low-gradient Johnson Creek, ID 1.800 (1972) (0.5%) reaches1 Everest and Chapman Mean densities in a higher Johnson Creek, ID 0.500 (1972) gradient (1.3%) reach1 Big Springs Creek, Values from end of summer in Bjornn (1978) 1.350 ID fully seeded reach Upper Lochsa Values from fully seeded Petrosky (1990) 1.080 River, ID reaches in <2% channels1,2 Upper Lochsa Values from fully seeded Petrosky (1990) 0.670 River, ID reaches in 2–4% channels1,3 1 Habitat type-specific values not reported 2 Gradient based on Rosgen C-channel designation 3 Gradient based on Rosgen B-channel designation

February 2012 Stillwater Sciences 41 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

6.1.1.5 Physical habitat thresholds To further refine carrying capacity estimates, physical thresholds can be used in the HAB module to specify channel reaches suitable for holding, spawning, and rearing. Life stage-specific thresholds that can be applied include minimum and maximum substrate size (D50), channel width, and channel depth as predicted by the GEO module. Of these, only channel width predictions were used to define the upstream and downstream extent of suitable habitat in the upper Yuba River RIPPLE application.

The HAB module calculates reach-specific carrying capacities for all life stages in reaches not excluded by physical habitat thresholds or water temperature (see Section 4). As described in Section 4, the upstream extent of spring-run Chinook salmon holding, spawning, and rearing habitat was restricted by applying minimum channel width thresholds used in combination with channel gradient thresholds. Channel gradient thresholds were applied through GIS analysis of the channel network and were not a threshold parameter within the HAB module. The downstream extent of potential habitat for each life stage was determined using water temperature criteria. The resulting downstream extent of suitable habitat was implemented in the HAB module by applying maximum channel width thresholds that correspond to the predicted channel width at the locations where temperatures became unsuitable.

6.1.1.6 Parameterization of Alternative Management Scenarios

The following table summarizes parameter changes resulting from alternative management scenarios.

Table 6-4. Parameters changed in the HAB module for spring-run Chinook salmon model runs for Alternative Management Scenarios 1 and 2 relative to current conditions. All other parameters were unchanged between scenarios. Sub- Alternative Management Alternative Management Parameters changed basins Scenario 1 Scenario 2 Maximum channel width SY and Increased to allow use of Increased to allow use of thresholds for holding, MY thermally suitable channels thermally suitable channels spawning, and rearing Changed to reflect holding Changed to reflect holding SY and Holding usable fraction pools quantity in thermally pools quantity in thermally MY suitable reach suitable reach

Spawning usable Increased to 50% of SY and Increased to match SY and NBB fraction MY values MY values

6.1.2 Results and discussion 6.1.2.1 Predicted distribution of suitable habitat Due to high water temperature, no suitable spring-run Chinook salmon habitat was predicted to occur in the SY sub-basin under current conditions (Map 4, Table 4-3, Figure 4-1). Under Alternative Management Scenario 1, suitable habitat in the SY sub-basin for holding, spawning, and summer rearing includes 7 miles of the mainstem South Yuba River (from the natural fish passage barrier downstream to the Poorman Creek confluence) and 3.3 miles of Canyon Creek. Under Alternative Management Scenario 2, 15.3 miles of habitat in the mainstem South Yuba

February 2012 Stillwater Sciences 42 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

River was predicted to be suitable (downstream to the Humbug Creek confluence). No additional tributary habitat was predicted under Alternative Management Scenario 2. Poorman Creek, Humbug Creek, and other tributaries to the South Yuba River were not considered suitable for spring-run Chinook salmon due to channel width restrictions that were set to exclude channels too small to provide suitable holding pools. This prediction is corroborated for the lower portion of Poorman Creek by Nikirk and Mesick (2006), who reported no suitable holding pools in the lowermost reaches of Poorman Creek when it was surveyed in summer 2003.

In the MY sub-basin, 2.3 miles of the mainstem Middle Yuba River was predicted to be suitable for spring-run Chinook salmon under current conditions (Map 4, Table 4-3, Figure 4-1). Due to channel width restrictions at the upstream end of the distribution, the predicted extent of suitable habitat in the Middle Yuba River under current conditions does not extend upstream to the natural fish passage barrier. Under Alternative Management Scenario 1, 11.9 miles of the mainstem Middle Yuba River would be suitable for holding, spawning, and summer rearing. Suitable habitat under Scenario 1 was predicted to extend from the upstream migration barrier at RM 35.1 downstream to RM 23.2. Suitable habitat under Scenario 2 was predicted to extend downstream to Our House Dam at RM 12.5, an increase of 10.6 miles relative to Scenario 1. Increased flows under both alternative management scenarios were predicted to result in a greater summer channel width than under current conditions, which is sufficient to provide suitable spring-run Chinook salmon holding habitat upstream to the natural migration barrier. No tributary habitat in the MY sub-basin was predicted to be suitable under either Scenario 1 or Scenario 2.

The extent of suitable habitat for spring-run Chinook salmon in the NY sub-basin under current conditions was predicted to be greater than in any of the other sub-basins (Map 4, Table 4-3, Figure 4-1). Habitat predicted to be suitable for holding, spawning, and summer rearing under current conditions in the NY sub-basin includes 27.7 miles of the mainstem North Yuba River (from the natural passage barrier at RM 51 downstream to RM 23), 1.8 miles of the Downie River, 3.8 miles of Lavezzola Creek, and 1.4 miles of Haypress Creek. The upstream extent of suitable habitat in the Downie River, and Lavezzola Creek was restricted by channel width. The upstream extent of suitable habitat in Haypress Creek was restricted by channel gradient. Slate Creek and Canyon Creek were not considered suitable for spring-run Chinook salmon under current conditions due to prohibitively high water temperatures. Other tributaries to the North Yuba River were not considered suitable for spring-run Chinook salmon due to channel width or gradient restrictions. Alternative management scenarios were not modeled for the NY sub-basin.

In the NBB sub-basin, habitat predicted to be suitable for spring-run Chinook salmon holding and summer rearing under current conditions is limited to 3.2 miles of the mainstem (Map 4, Table 4- 3, Figure 4-1). Suitable habitat under current conditions is located where summer water temperatures are consistently cool enough to support these life stages—1.2 miles of the mainstem North Yuba River downstream of New Bullards Bar Dam and 2 miles of the mainstem Yuba River downstream of New Colgate Powerhouse. Under Alternative Management Scenarios 1 and 2, water temperatures would be cool enough to provide suitable habitat for the entire 10.3 miles of mainstem habitat downstream of New Bullards Bar Dam. No tributary habitat in the NBB sub- basin was predicted to be suitable for spring-run Chinook salmon under current conditions or either of the alternative management scenarios.

6.1.2.2 Carrying capacity estimates The HAB module output demonstrates that in all modeled sub-basins and scenarios, the carrying capacity of holding habitat exceeds that of redd carrying capacity in reaches with potentially suitable habitat (Table 6-5). In all cases, predicted holding capacity (males and females) is more

February 2012 Stillwater Sciences 43 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed than twice that of predicted redd capacity (females only). This result suggests that, when adult female escapement to freshwater and survival during holding are high enough to produce female spawners in excess of the redd carrying capacity, the quantity of spawning habitat likely limits production of juvenile and smolt emigrants from the upper Yuba River watershed.

Table 6-5. Predicted habitat carrying capacities of spring-run Chinook salmon holding, spawning (redds), and summer rearing life stages for each modeled sub-basin and scenario in the upper Yuba River watershed.

Carrying Capacity South Middle North Scenario1 NBB (K) Yuba2 Yuba Yuba3 CC 0 2,613 15,597 4,069 Holding S1 9,729 10,973 n/a 20,307 S2 19,054 17,100 n/a 20,307 CC 0 126 2,696 123 Redd4 S1 707 929 n/a 889 S2 1,621 2,098 n/a 1,777 CC 0 8,493 766,391 282,393 Age-0 summer S1 143,747 138,392 n/a 621,992 rearing S2 522,295 394,821 n/a 621,992 1 CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2. 2 Under current conditions the entire SY below the natural fish passage barrier was predicted to be thermally unsuitable for spring-run Chinook salmon holding and rearing; therefore carrying capacity is zero. 3 Alternative management scenarios were not modeled for the North Yuba sub-basin. 4 Each redd was assumed to support one female spawner.

In the SY sub-basin, redd capacity under Alternative Management Scenario 2 was predicted to be more than twice that of Alternative Management Scenario 1 (Table 6-5, Figure 6-1). In the MY sub-basin, predicted redd capacity under Alternative Management Scenario 1 is over seven times higher than current conditions, but less than half of Alternative Management Scenario 2, which was predicted to support nearly 17 times more redds than current conditions. In each case, the predicted increases are attributable primarily to the increase in suitable holding and spawning habitat that would result from increased summer flow (Map 4, Table 4-3). The predicted redd capacity increases are also partly related to the increase in wetted width (Section 5.2.2), and thus potential inundation of spawning gravels, associated with increased stream flows under the alternative management scenarios. In the NBB sub-basin, the predicted increases in redd capacity under Alternative Management Scenarios 1 and 2 are approximately 7 and 14 times higher than current conditions, respectively. In this sub-basin, the doubling of redd capacity between Alternative Management Scenarios 1 and 2 reflects the difference between partial and full restoration of spawning habitat specified for each scenario (Section 4). In the NBB sub-basin, it was assumed that all restored spawning gravel under the alternative management scenarios would be located in reaches where water temperatures are suitable for holding and spawning.

February 2012 Stillwater Sciences 44 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

3,000

CC S1 S2 2,500

2,000 redds

of 1,500 Number 1,000

500

0 South Yuba Middle Yuba North Yuba NBB Figure 6-1. Predicted habitat carrying capacity of spring-run Chinook salmon redds under current conditions and two modeled scenarios. Alternative management scenarios were not modeled for the North Yuba sub-basin. CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2.

In the NY sub-basin, predicted redd capacity and age-0 summer rearing capacity under current conditions were substantially greater than the MY and SY sub-basins, even when compared with predicted MY and SY carrying capacities under the alternative management scenarios (Table 6- 5). The NY sub-basin was predicted to support approximately 29% and 66% more redds under current conditions than the MY and SY sub-basins, respectively, would support under Alternative Management Scenario 2 (Table 6-5). Predicted holding habitat capacity in the NY sub-basin exceeds the predicted holding capacity in the SY and MY under current conditions and Scenario 1. Only under Scenario 2 does predicted holding capacity in the MY and SY sub-basins equal or exceed the NY sub-basin. Despite a lower density of pool habitat in the NY as compared with the SY and MY (Appendix F, Table F-1), the greater redd capacity of the NY can be attributed to a substantially longer length of potentially suitable channel habitat (Map 4). The lower pool frequency of the NY also explains why holding capacity in the NY under current conditions is not significantly greater than holding capacity in the SY and MY under Alternative Management Scenario 2.

Carrying capacity for the age-0 summer rearing life stage reflects the relative potential of each sub-basin to provide over-summering habitat and produce yearling spring-run Chinook salmon smolts (“smolt 1” in the POP module). Predicted habitat for age-0 summer rearing in the NY sub- basin under current conditions is 1.5 times greater than that predicted in the SY under Scenario 2, approximately 1.9 times greater than that predicted in the MY under Scenario 2, and approximately 1.2 times greater than that predicted in the NBB sub-basin under both alternative

February 2012 Stillwater Sciences 45 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed management scenarios (Table 6-5). As described above, the predicted NY rearing capacity would be even greater if not for the relatively low frequency of pools in the NY compared with the other sub-basins. In the SY, MY, and NBB sub-basins, age-0 summer rearing capacity increased markedly under the alternative flow scenarios compared with current conditions (Table 6-5). This results from an increased length of thermally suitable channel and greater area of channel inundated during the summer low flow period, as discussed in Section 5.2.2. The relatively high age-0 summer juvenile carrying capacity predicted for the NBB sub-basin compared to the MY and SY sub-basins under Alternative Management Scenarios 1 and 2 can be attributed to the significantly wider summer low flow channel, which results in a greater area of rearing habitat. Age-0 summer rearing capacity did not increase in the NBB between Alternative Management Scenarios 1 and 2, since the only difference between scenarios was augmentation of spawning gravels.

6.2 Population Dynamics (POP) 6.2.1 POP module structure The POP module uses reach-specific carrying capacity (K) values for holding, spawning, and summer rearing in conjunction with biological input parameters and life stage-specific stock- production curves6, to estimate equilibrium population sizes for individual channel arcs and the entire watershed. The equilibrium population is reached after multiple iterations of the model are run and a stable, long-term average population structure is reached. Figure 6-2 displays a schematic diagram of the POP module structure, and Table 6-6 describes the life stages used in the spring-run Chinook salmon model input and output.

6 Only two stock-production rules are currently used in the Chinook model: (1) the “hockey stick”: if the starting population is x, the ending population is the smaller of rx and K, where K is the arc-specific carrying capacity and r is a density-independent survivorship; and (2) the “Skellam function”: if the starting population is x, the ending population is K(1-exp(rx/K)). The Skellam function is used only for calculating superimposition losses. All other density- dependent mortality calculations in the model use hockey-stock functions.

February 2012 Stillwater Sciences 46 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Figure 6-2. Schematic diagram showing the relationships between each life stage in the POP module and the point at which each carrying capacity (K) is applied to the population. BY = brood year.

Table 6-6. Life stages represented in the spring-run Chinook salmon POP module. POP module Description life stage Total number of all ages of immature adults leaving the ocean to search for holding escape habitat. holder Male and female adults occupying holding habitat. spawner Females leaving holding habitat in search of spawning habitat. Effective number of redds that contribute to egg production after accounting for the redd effects of superimposition. eggs Total number off eggs produced. swimup Fry emerging from redd gravels. Fry that leave the modeled channel network soon after emergence and rear in the lower efry mainstem river(s) and estuary prior to smolting. The “e” refers to estuary. Juvenile population remaining after efry have left the channel network that survive from summer0 fry to early summer. Component of the juvenile population that smolts during the spring and early summer of smolt0 their first year prior to leaving the channel network or while migrating downstream. Component of the juvenile population remaining, after smolt0 have left the channel winter1 network, that survive from summer to winter. Component of the juvenile population that smolts during the late fall through winter as smolt1 “yearlings.”

February 2012 Stillwater Sciences 47 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

POP module Description life stage Efry that survive the spring and early summer in the estuary to become smolts. The “e” esmolt0 refers to estuary. Ocean-resident fish that have spent X years in fresh water before smolting and Y years in oceanXY saltwater after smolting, respectively; “X+Y” is the total age. escapeXY Fish of age X+Y participating in the spawning run, at the time they leave the ocean.

The stages escape, holder, spawner, and redd include age-structure information: that is, the model keeps track of the brood-year composition of these stages so that age-specific versions of parameters like sex ratios and fecundities can be applied.

In the POP module, the stage escape represents sexually immature adults leaving the ocean to search for holding habitat. The stage holder represents adults (both male and female) occupying holding habitat. Holder was calculated by distributing the escaped population across accessible arcs of the channel network in proportion to the capacity of these arcs (given by holding_K; Figure 6-2), applying a density-independent survival parameter (holding_survival), and truncating any excess to the carrying capacity. Refer to Appendix G for a description of each parameter required for input in POP module. The stage spawner represents females at the spawning habitat. Spawner was calculated by multiplying by the holder population of each age by the parameter fraction female for each age. The spawning stage females were then distributed across accessible arcs of the channel network in proportion to the capacity of these arcs (given by redd_K; Figure 6-2). The redd stage represents the number of redds that contribute to egg production after accounting for spawning carrying capacity (redd_K) and the effects of superimposition. The number of eggs produced by all redds was calculated by applying the age-specific parameter eggs per female for each successfully spawning female.

The number of emergent fry (swimup) was calculated by multiplying the number of eggs by the embryo survival parameter (Appendix G). The swimup population was then partitioned into prospective efry (i.e., estuary-bound fry) and resident fry according to the parameter efry fraction. The number of estuary-bound fry that survive to leave the modeled channel network, becoming efry, was determined from the survival parameter, swimup to efry survival (Appendix G). The efry that survive in the lower river and delta, determined from the parameter efry to esmolt0 survival (Appendix G), were transformed into to smolts designated as esmolt0.

The swimup fry remaining in the channel network (non-efry) experience density-independent survival (fry to summer0 survival) to become summer0. The summer0 then redistribute downstream in search of available habitat, which was determined by age-0 summer_K (Figure 6- 2). Summer0 migrants that reach the bottom of the modeled stream network without finding summer rearing habitat become smolt0.

The remaining summer0 (those that find over-summering habitat) experience density-independent survival (summer0 to winter1 survival) to become winter1. All winter1 in the upper Yuba River spring-run Chinook salmon model leave the channel network as yearlings called smolt1. Survival of smolt0 and smolt1 until adult escapement from the ocean to freshwater was determined using the parameters smolt0 to adult survival and smolt1 to adult survival, respectively (Appendix G). Survival of esmolt0 until adult return was also determined by the smolt0 to adult survival model parameter.

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The POP module recognizes 10 life stages of ocean-resident fish, designated oceanXY for X=0 or 1, Y=0, 1, 2, 3, or 4. The “X” and “Y” indicate the number of years spent in freshwater before smolting and in saltwater after smolting, respectively; “X+Y” is the total age. The stages ocean00, ocean10, ocean01, and ocean11 represent fish too small to be harvested or to join a spawning run. The stages oceanXY for Y>1 represent the total populations of fish of age X+Y in the ocean, at a time shortly before the start of the spawning migration. The stages escapeXY represent the fish of age X+Y participating in the spawning run, at the time they leave the ocean. These were calculated as the product of oceanXY and the spawning_fraction of each age in the spawning run (Appendix G). For convenience, the model reports the total number of “escapers” of all ages as escape.

6.2.2 POP module parameterization The POP module parameter values applied in the model and the data sources and rationale used for their selection are shown in Appendix G. These parameters were applied to all upper Yuba River watershed model runs and scenarios. Where possible, we used biological parameters specific to spring-run Chinook salmon populations in the upper Sacramento River basin.

6.2.3 Results and discussion Table 6-7 shows equilibrium population sizes of key spring-run Chinook salmon life stages predicted by the POP module for each upper Yuba River sub-basin and scenario. At the moderate smolt-to-adult survival parameter values used (Appendix G), predicted adult escapement (escape) was sufficient to fully seed available habitat for most model runs. However, holding habitat was not fully seeded in the SY sub-basin under Alternative Management Scenario 1 or in the MY and NBB sub-basins under current conditions (that is, holder predicted by POP was lower than holding_K predicted by HAB; Table 6-5). Notably, spawning habitat, which is more limiting than holding habitat, was fully seeded in all model runs. In each sub-basin and each scenario, the predicted number of spawners was greater than redds (Table 6-7), indicating that predicted adult escapement was sufficient to fully seed the available spawning habitat (Table 6-5). This result, in turn, indicates that smolt production estimates represent the maximum production potential at the freshwater survival parameter values used (Appendix G).

Table 6-7. Predicted equilibrium population sizes for select spring-run Chinook salmon life stages for each modeled sub-basin and scenario in the upper Yuba River watershed.

Model Life stage South Yuba2 Middle Yuba North Yuba NBB scenario1 CC 0 633,541 13,212,106 633,204 egg S1 3,596,933 4,709,035 n/a 4,558,997 S2 8,279,491 10,554,651 n/a 9,058,929 CC 0 481,491 10,041,200 481,235 swimup S1 1,942,344 3,578,866 n/a 3,464,838 S2 4,470,925 8,021,535 n/a 6,884,786 CC 0 180,559 3,765,450 180,463 efry S1 728,379 1,342,075 n/a 1,299,314 S2 1,676,597 3,008,076 n/a 2,581,795

February 2012 Stillwater Sciences 49 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Model Life stage South Yuba2 Middle Yuba North Yuba NBB scenario1 CC 0 76,125 991,281 0 smolt0 S1 199,272 489,130 n/a 0 S2 263,584 1,010,276 n/a 582,808 CC 0 5,675 535,920 58,951 smolt1 S1 98,366 95,894 n/a 424,421 S2 363,019 275,223 n/a 435,378 CC 0 1,532 46,876 3,435 escape S1 8,878 13,310 n/a 24,729 S2 25,314 31,986 n/a 34,568 CC 0 1,379 15,597 3,091 holder S1 7,990 10,973 n/a 20,307 S2 19,054 17,100 n/a 20,307 CC 0 752 8,733 1,765 spawner S1 4,468 6,054 n/a 11,595 S2 10,776 9,481 n/a 11,416 CC 0 125 2,591 123 redds S1 706 927 n/a 889 S2 1,619 2,075 n/a 1,774 1 CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2. 2 Under current conditions the entire SY below the upstream migration barrier was predicted to be thermally unsuitable for spring-run Chinook salmon holding and rearing; therefore production of each life stage is zero.

The POP module results further indicate that, in nearly all model runs, swimup production from available spawning gravels is sufficient to fully seed the age-0 summer rearing habitat (age-0 summer0_K) with individuals destined to become smolt1. That is, sufficient summer0 remain after multiplying swimup by the efry fraction of 0.75 (Appendix G) to exceed age-0 summer0_K. In contrast, age-0 summer rearing habitat is not fully seeded in the NBB sub-basin under current conditions or Alternative Management Scenario 1 due to the limited quantity of spawning gravels in these scenarios. Since the number of smolt0 produced is determined by the number of summer0 in excess of age-0 summer0_K, this explains why zero smolt0 were produced under these scenarios (Table 6-7).

Compared with current conditions, production of efry, smolt0, and smolt1 from each sub-basin was predicted to increase substantially (Figure 6-3). This increased production is a result of a greater amount of spawning and age-0 summer habitat available (Map 4, Table 6-5). Increased production of the important stream-type smolt1 life history component under alternative management scenarios was particularly notable. For example, in the MY sub-basin estimated production of smolt1 under Alternative Management Scenarios 1 and 2 was approximately 17 and 49 times higher, respectively, than under current conditions. In the SY sub-basin, smolt1 production under Alternative Management Scenario 1 was nearly 4 times higher than under Alternative Management Scenario 2. Finally, in the NBB reach, the number of smolt1 produced under Alternative Management Scenarios 1 and 2 was approximately 7.2 and 7.4 times higher, respectively, than current conditions.

February 2012 Stillwater Sciences 50 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

1,600,000

1,400,000 smolt0 smolt1 1,200,000

1,000,000 smolt

of 800,000

600,000 Number

400,000

200,000

0 SY‐CC SY‐S1 SY‐S2 MY‐CC MY‐S1 MY‐S2 NY‐CC NBB‐CC NBB‐S1 NBB‐S2 Figure 6-3. Predicted equilibrium population sizes for different aged spring-run Chinook salmon smolts under current conditions and two modeled scenarios. Alternative management scenarios were not modeled for the North Yuba sub-basin. CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2.

Smolt1 production in the sub-basins was directly proportional to age-0 summer carrying capacity. As expected by the higher age-0 summer carrying capacities predicted by the HAB module (Table 6-5), production of smolt1 was higher in the NY sub-basin compared with the other sub- basins: approximately 1.5 times, 1.9 times, and 1.2 times higher than the SY, MY, and NBB sub- basins, respectively, under Alternative Management Scenario 2 (Table 6-7, Figure 6-3).

The POP module output also allows an estimate of the fraction of each juvenile life history type produced in each sub-basin and scenario (Table 6-8). The fraction of each juvenile life history type is important to the dynamics and viability of each population due the expected increase in delta and ocean survival with increasing size and age (Reisenbichler et al. 1982, Brandes and McLain 2001) and thus the relative contribution of each juvenile life history type to the returning adult population. The relative contribution of efry to juvenile production is similar between all scenarios, varying between 69% and 75% (Table 6-8) of the juvenile production. The fraction of the smolt0 population varied from 0% in the NBB sub-basin to approximately 30% in the MY sub-basin under current conditions. The fraction of smolt1 varied between approximately 2% in the MY sub-basin under current conditions and 25% in the NBB sub-basin.

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Table 6-8. Percent of total predicted spring-run Chinook salmon juvenile production composed of efry, smolt0, and smolt1 life history types for each modeled reach and scenario in the upper Yuba River watershed. CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2.

Juvenile Model South Middle North life NBB scenario Yuba Yuba Yuba history CC n/a 68.8% 71.1% 75.4% Efry S1 71.0% 69.6% n/a 75.4% S2 72.8% 70.1% n/a 71.7% CC n/a 29.0% 18.7% 0.0% Smolt0 S1 19.4% 25.4% n/a 0.0% S2 11.4% 23.5% n/a 16.2% CC n/a 2.2% 10.1% 24.6% Smolt1 S1 9.6% 5.0% n/a 24.6% S2 15.8% 6.4% n/a 12.1%

The adult escapement estimates (“escape”) generated by the POP module (Table 6-7) provide only a rough estimate of the number of adults that likely to return to each sub-basin under equilibrium population conditions. However, preliminary model gaming suggests that there would be sufficient adult escapement to fully seed the available spawning habitat at much lower smolt-to-adult survival values; thus we do not consider that the number of adults predicted would affect our smolt and juvenile production estimates. Notwithstanding these considerations, the primary objective of the model was to predict freshwater habitat capacity of holders, spawners, and juveniles and to estimate production of juveniles and smolts. The model results and discussion will serve as data inputs to a statistical model downstream of Englebright Dam to characterize Delta and ocean conditions.

Under current conditions, unsuitably high water temperatures would limit access by reintroduced spring-run Chinook salmon to over 30 miles of otherwise high quality mainstem spawning and rearing habitats in the SY and MY sub-basins, greatly limiting potential smolt production. Similarly, high water temperatures in the NBB sub-basin would restrict spawning and juvenile rearing to a fraction of otherwise suitable habitat, and lack of spawning gravel in thermally suitable reaches would further limit juvenile production. Nonetheless, model results indicate that, in the North Yuba River under current conditions and the SY, MY, and NBB sub-basins under the alternative management scenarios, sufficient spring-run Chinook salmon holding, spawning, and rearing habitat exists to allow for production of substantial numbers of juveniles and smolts.

6.3 Chinook Salmon Model Sensitivity and Uncertainty The accuracy of model projections is affected by how data availability, data quality and model structure affect the degree of uncertainty in model parameters. The level of importance of the uncertainty of different parameters depends on the degree to which parameters affect the predictions that are necessary to meet project objectives (i.e., model sensitivity to parameters). If the uncertainty of a parameter directly affects our conclusions regarding key project objectives, then it warrants further analysis. In the model development for this study, we focused our assessment of model sensitivity on parameter values likely to change model results. Parameters with a low level of certainty and high level of sensitivity were recommended for additional

February 2012 Stillwater Sciences 52 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed sampling. As described in Section 8, systematic model gaming, validation, and refinement are recommended to enhance model predictions. The following are some of the key uncertainties in sensitive model parameters for the spring-run Chinook salmon RIPPLE model:  The parameter efry fraction determines both the numbers of efry and directly affects both the number of smolt0 and smolt1 produced. For example, in scenarios where age-0 summer carrying capacity is not fully seeded, efry fraction will produce no smolt0 and fewer smolt1. Since efry have much lower delta and ocean survival than smolt0 and smolt1 life histories, increasing the efry fraction would reduce the number of adults returning to freshwater. Consequently, it would be much more difficult to fully seed the available spawning habitat. In contrast, lowering efry fraction would result in higher numbers of smolt0 and therefore increase adult escapement. Accurate data on the fraction of the juvenile population comprised of each life history is difficult to collect. Some portion of downstream movement by efry may be volitional, but the number of fry moving downstream also likely depends on flow levels and water temperature: in years with high flows a greater fraction of emergent fry would likely be displaced downstream (Healey 1991). Furthermore, most smolt trapping data are not reliable for accurately calculating the relative magnitude of juvenile life history types since traps often have to be removed during winter flow events, when unknown numbers of fish are moving.  Model results are also particularly sensitive to smolt-to-adult survival parameters. For example, very poor delta and ocean conditions could result in escapement levels lower than that required to fully seed spawning habitat in all years. However, given the primary model objective of calculating potential carrying capacity and smolt production, there was not sufficient justification to lower ocean survival parameters to levels that might produce a low number of returning adults. Furthermore, preliminary model gaming suggests there would be sufficient adult escapement to fully seed available spawning habitat at much lower smolt-to-adult survival values than those used; thus estimates of smolt and juvenile production potential are deemed reliable. Further model gaming could be used to determine the minimum smolt-to-adult survival values required to fully seed spawning habitat in each sub-basin. Refinement of adult escapement estimates will be possible following additional modeling outside of RIPPLE to simulate more realistic survival estimates downstream of Englebright Dam.  Juvenile mortality due to predation in Englebright Reservoir and the lower reaches of each sub-basin is currently not included in the model projections. We recommend additional study to further explore the potential effects of predation on spring-run Chinook salmon survival and production.

7 STEELHEAD

7.1 Model Assumptions and Structure We modeled steelhead carrying capacity the upper Yuba River watershed using the RIPPLE HAB module. In keeping with the objectives and scope of this project, we did not parameterize and run the POP module for steelhead due to an acknowledged lack of data and the complexity of steelhead life history. Instead, potential smolt production was estimated as a function of the carrying capacity and density-independent mortality that occurred after the limiting life stage.

We modeled carrying capacity for steelhead spawning, age 1+ summer, and age 1+ winter habitats, but did not model carrying capacity for age-0 juvenile steelhead in their first summer and winter. We made the simplifying assumption that juvenile habitat for age 1+ would be more

February 2012 Stillwater Sciences 53 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed limiting than age-0 juvenile habitat in both seasons, which was consistent with evidence from various studies of steelhead limiting factors (Stillwater Sciences 2006d, 2007, Greenspace-The Cambria Land Trust et al. 2011). As juvenile steelhead grow, they require more space for foraging and cover (Bjornn and Reiser 1991, Stillwater Sciences 2008), and in the summer age-0 steelhead can use shallower and slower habitat with finer substrates (e.g., gravels) to meet their energetic demands and escape predators. In contrast, larger sized age 1+ steelhead become increasingly territorial (Keeley 2000), have higher energetic demands, and require deeper, more complex pools and coarser substrate for cover while feeding (Hartman 1965, Fontaine 1988, Spina 2003). Likewise, in the winter, smaller age-0 fish can utilize a wider range of substrate sizes for refuge. For this reason, in the winter, habitat is expected to become unsuitable for age 1+ steelhead at lower magnitudes of sedimentation than for age-0 steelhead. In summary, a stream reach can support far fewer age 1+ than age-0 individuals during both summer and winter, due to the greater area of shallow habitats available, and because age-0 steelhead can generally utilize habitat suitable for age 1+ steelhead, but age 1+ steelhead can not use the shallower, finer substrate habitat suitable for age-0.

As discussed in Section 2.2, the length of time steelhead spend rearing in freshwater varies considerably. However, in our prediction of smolt production potential based on age-1+ juvenile carrying capacity we made the simplifying assumption for the model that the majority of the steelhead population in the upper Yuba River watershed will emigrate as 2-year-olds following their second winter in freshwater. This assumption is consistent with data and assumptions reported by Hallock et al. (1961) and McEwan (2001).

7.2 Habitat Capacity (HAB) 7.2.1 Methods 7.2.1.1 Channel gradient and habitat type composition As described Section 6.1.1.1 the first step in applying HAB was to determine the channel gradient classes that equate to reaches with different morphology and, consequently, differing habitat quality and quantity for each life stage of the focal species. The same gradient classes used for spring-run Chinook salmon model were used for the steelhead model. Gradients greater than 12% were not considered steelhead habitat, but short reaches (< 300 m) with gradients up to 20% were included in the modeled channel networks. As described in Section 4, we assumed that steelhead could pass these short, steep reaches to utilize lower gradient habitats upstream to the known passage barriers in the mainstems of each sub-basin or to the upstream extent of habitat in tributaries defined by channel with or gradient thresholds (see Section 4).

As with the spring-run Chinook salmon model, the HAB module requires life stage-specific data on habitat type composition, fish density, fraction of habitat usable, and suitable channel widths, depths, and substrate sizes for each channel gradient class. These data were derived from the best available sources, including published literature, unpublished reports, and field data collected in the upper Yuba River watershed, if available. Table 6-1 describes the HAB module input parameters required for steelhead.

The same habitat type fraction values used for the spring-run Chinook salmon model were also used to parameterize the steelhead model for each sub-basin. Section 6.2.1.1 describes the methods used to derive habitat type fraction values and Appendix F, Table F-1 shows the values used.

February 2012 Stillwater Sciences 54 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

7.2.1.2 Spawning density and usable fraction Data on steelhead spawning density in the upper Yuba River basin were not available; therefore spawning density was calculated based on mean redd sizes measured in the American River and South Fork Eel River tributaries, which were approximately 2.0 m2 and 1.5 m2, respectively (Trush 1991, Hannon and Deason 2007). Assuming one female per redd, these redd sizes equates to spawning densities of 0.50 and 0.66 females per m2, respectively. The spawning density calculated from redd sizes in the larger, more alluvial American River was used to parameterize 0–1 and 1–2% gradient categories, which are more prevalent in the large mainstem habitat of the upper Yuba River sub-basins. The spawning density calculated from redd sizes in the smaller, higher gradient South Fork Eel River tributaries was used to parameterize the 2–4 and 4–8% gradient classes in the upper Yuba River sub-basin.

Usable fraction of the channel suitable for steelhead spawning was calculated for each gradient category and habitat type combination by dividing the area of suitable steelhead spawning gravel by the total channel area. Suitable spawning gravel area for steelhead in each gradient class in the South and Middle Yuba rivers and the mainstem Yuba River in the NBB sub-basin was calculated from spawning gravel data collected by Nikirk and Mesick (2006). We omitted all gravel patches with median grain size less than 10 mm and greater than 50 mm from estimates, assuming they were unsuitable for steelhead spawning (Kondolf and Wolman 1993). In contrast to the methods used to calculate spring-run Chinook salmon spawning gravel area, we included gravel area measured on the floodplain adjacent to pools, which was expected to be inundated during the steelhead spawning season. The estimated amount of spawning gravel area was then apportioned among habitat types in the 0–4% gradient classes by assuming 80% of spawning gravel was in pools, 10% in riffles, 10% in runs, and 0% in cascades. This assumption was based on professional opinion and evidence from the literature that most spawning occurs in pool tails (Barnhart 1991, CDFG 1998a, b) in lower gradient reaches. In gradients of 4–8% we assumed 100% of spawning occurs in pools. Although rearing can occur at gradients up to 12%, we assumed steelhead spawning did not occur in reaches with gradients > 8%. Total channel area for each gradient and habitat type class was calculated using GIS channel gradient data and the RIPPLE GEO output of winter base flow width. Since spawning habitat data were not available for the North Yuba, the usable fraction values calculated from South and Middle Yuba spawning habitat data were applied to the North Yuba. For the SY, MY, and NY model runs, the same spawning parameter values were used for all scenarios (Appendix H, Table H-1).

In the NBB sub-basin, the usable fraction of spawning habitat under current conditions was calculated as described above for the South and Middle Yuba rivers. In their evaluation of spawning habitat, Nikirk and Mesick (2006) did not observe suitable steelhead spawning habitat in the NBB reach upstream of the Middle Yuba confluence. Therefore, spawning capacity of this reach was set to zero for current conditions. As described in Section 4, Alternative Management Scenarios 1 and 2 assume gravel augmentation would take place in the Yuba River below New Bullards Bar Dam, which was simulated in the NBB model run by increasing the usable fraction of spawning. It was assumed that the quantity of spawning gravels measured in the South and Middle Yuba rivers represents a reasonable target for spawning habitat restoration and thus we applied usable fraction values calculated for these sub-basins to NBB Scenario 2. Scenario 1 values were calculated as 50% of each usable fraction value used in Scenario 2. Spawning density and usable fraction values used in the NBB model runs for each sub-basin are shown in Appendix H, Table H-2.

February 2012 Stillwater Sciences 55 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

7.2.1.3 Summer juvenile rearing density and usable fraction In the steelhead RIPPLE model, summer carrying capacity for age 1+ juveniles was calculated as the product of density, usable fraction, and summer low flow channel area predicted by the GEO module (Section 5). The resulting values were used to parameterize the steelhead HAB module for all sub-basins and model runs. Age 1+ summer densities for each model run were independently parameterized for larger “mainstem” channels (represented for modeling purposes by channels with gradients of 0–1% and 1–2%) and for smaller channels and tributaries (represented for modeling purposes by channels with gradients of 2–4%, 4–8%, and 8–12%). Based on the predicted channel gradient in all sub-basins of the Upper Yuba River watershed, channels with gradients less than 2% provide a close approximation of the extent of mainstem channel habitat in each sub-basin downstream of the impassable barriers (Map 3). In contrast, the steeper gradient channels (≥ 2%) represent most tributaries and the smaller, higher elevation stream reaches. The steelhead HAB module was parameterized using different summer densities for the larger mainstem reaches based on the following rationale: (1) the most spatially comprehensive and quantitatively derived summer O. mykiss density data available for the Upper Yuba River watershed (NID and PG&E 2009) were collected in mainstem reaches of the South, Middle, and North Yuba rivers (only limited quantitative data were available for tributaries of the South, Middle, or North Yuba rivers), and (2) evidence from a variety of studies suggests that O. mykiss summer densities (habitat type-specific densities as well as ratios of densities among habitat types) in larger mainstem habitats can differ substantially from those in smaller channels and tributaries (Table 7-1).

Table 7-1. Habitat type-specific summer rearing densities reported for age 1+ juvenile steelhead.

Channel Data Density (fish/m2) Source Notes size location Pool Riffle Run Mean of electrofishing data collected at seven sites in the Upper Yuba NID and PG&E 0.121 mainstem South, Middle, and North River (2009) Yuba rivers during July and August 20081. July and August 2004 snorkel data. Middle Densities of 4–8" O. mykiss in MY Gast et al. (2005) 0.006 0.030 0.022 Yuba River upstream of RM 17.0, calculated from raw survey data. July and August 2004 snorkel data. South Yuba Densities of 4–8 in O. mykiss in SY Gast et al. (2005) 0.020 0.017 0.022 River upstream of RM 18.1, calculated from raw survey data.

Larger mainstem rivers rivers mainstem Larger Calaveras, Stillwater Sciences Snorkel data, collected in pools and 0.080 n/a 0.090 River, CA (2004) runs only.

Snorkel data, collected in pools and South Scarnecchia and riffles only; mean of August Umpqua 0.032 0.034 n/a Roper (2000) densities from four mainstem River, OR reaches.

February 2012 Stillwater Sciences 56 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Channel Data Density (fish/m2) Source Notes size location Pool Riffle Run Upper Stillwater Sciences Snorkel data; tributary to Coyote Penitencia 0.108 0.054 0.057 (2006d) Creek, Santa Clara County. Creek, CA Electrofishing data, collected in Devil’s Stillwater Sciences 0.121 n/a 0.016 pools and runs only; tributary to Gulch, CA (2008) Lagunitas Creek, Marin County. Electrofishing data, collected in Bear Creek, Connor (1996) 0.125 0.030 n/a pools and riffles only; tributary to CA Mattole River, Humboldt County. South Fork Electrofishing data, collected in Eel River pools and riffles only; mean of pool Connor (1996) 0.105 0.05 n/a tributaries, and riffle densities from four CA tributaries.

Smaller streams and tributaries South Snorkel data, collected in pools and Umpqua Scarnecchia and riffles only; mean of pool and riffle River 0.055 0.022 n/a Roper (2000) densities from nine upper basin tributaries, tributaries. OR 1 Habitat type-specific data not available.

Portions of the stream network with predicted gradients less than 2% were parameterized using steelhead densities from quantitative electrofishing data collected by YBDS relicensing participants at seven sites in the mainstem South, Middle, and North Yuba rivers during July– August 2008 (NID and PG&E 2009). We calculated densities (fish/m2) for each of the seven electrofishing sites using population estimates for age 1+ O. mykiss and site dimensions reported for each site. The mean density of the seven sites (0.121 fish/m2) was used in the RIPPLE HAB module to parameterize the lower channel gradient classes (0–1% and 1–2%) in all sub-basins. The NID and PG&E (2009) density estimates were not reported by habitat type; thus to parameterize the HAB module for channel gradients < 2%, we apportioned these density values into pools, riffles, and runs based on habitat type-specific density values for O. mykiss in the 4– 8 in (102–204 mm) size class reported by Gast et al. (2005) for the South and Middle Yuba rivers (Table 7-1). Of the O. mykiss size classes reported by Gast et al. (2005), the 4–8 in (102–204 mm) size class corresponds most closely to the size of 1 year-old (i.e., age 1+) O. mykiss documented in other streams in northern California (e.g., Lagunitas Creek and tributaries [Ettlinger et al. 2006]; tributaries to the Napa River [Stillwater Sciences 2007b]). Appendix H, Table H-3 provides the values used for each sub-basin, gradient class, and habitat type and illustrates how the YBDS electrofishing density values (NID and PG&E 2009) were apportioned into habitat type-specific densities. Juvenile rearing densities and usable fractions were not changed between model runs for the different scenarios.

Portions of the stream network with predicted gradients of 2% or greater were parameterized using the average of age 1+ O. mykiss summer densities reported for pools, riffles, and runs in tributary streams in northern California (Upper Penitencia Creek [Stillwater Sciences 2006d], Devil’s Gulch [Stillwater Sciences 2008], tributaries to the South Fork Eel and Mattole rivers [Connor 1996]) and tributaries to the South Umpqua River, Oregon (Scarnecchia and Roper 2000) (Table 7-1). These streams were chosen because we consider them representative of tributary streams with high quality steelhead habitat, and because they are among the few such

February 2012 Stillwater Sciences 57 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed streams for which habitat-specific density data for age 1+ steelhead are available. The average densities used to parameterize the steelhead HAB module for channels ≥ 2% were 0.104 fish/m2 for pools, 0.044 fish/m2 for riffles, and 0.037 fish/m2 for runs.

Densities of age 1+ O. mykiss from the YBDS electrofishing surveys (NID and PG&E 2009) were selected because they represented the most quantitative data available from the upper Yuba River watershed for predicting summer carrying capacity. Densities calculated from snorkel data collected by were much lower than values calculated from the YBDS electrofishing data (NID and PG&E 2009). We used the YBDS electrofishing density data based on the assumption that the electrofishing surveys provided a more robust estimate of densities for summer carrying capacity than the available snorkel survey data collected by Gast et al. (2005) and NID and PG&E (2009). However, it should be acknowledged that the YBDS electrofishing density data were derived from a small data set (seven sites: two in the South Yuba River, three in the Middle Yuba River, and two in the North Yuba River) collected during a single summer, and thus may not be representative of the true range of O. mykiss summer carrying capacities in the Upper Yuba River sub-basins. The age 1+ summer O. mykiss densities at the two YBDS electrofishing sites in the North Yuba River (0.223 and 0.396 fish/m2; mean = 0.310 fish/m2) were quite high relative to the densities at the five YBDS electrofishing sites in the South and Middle Yuba rivers (mean = 0.045 fish/m2; range: 0.010–0.079 fish/m2) (NID and PG&E 2009), but we used the overall mean of the seven electrofishing sites because we had no basis by which to determine whether the differences among sub-basins were truly representative of different carrying capacities or rather were anomalies resulting from low sample sizes, relatively poor spatial coverage of each sub-basin, and a single year of data. Given the uncertainties in summer rearing densities and the potential to significantly affect model predictions, we recommend additional sampling to collect habitat type-specific and gradient class-specific O. mykiss summer rearing density data in the mainstem North Yuba River and tributary streams in all three sub-basins of the upper Yuba River watershed.

7.2.1.4 Winter juvenile rearing density and usable fraction Winter carrying capacity for age-1+ juvenile steelhead was calculated in the HAB module as the product of density, usable fraction and winter base flow channel area predicted by the GEO module (Section 5). For all model runs, winter density was parameterized with a value of 5.5 fish/m2 (0.511 fish/ft2), which is (approximately) the average 1+ steelhead density in the coarsest substrate treatments reported by Meyer and Griffith (1997) following instream experiments evaluating the effects of substrate composition and winter habitat quality on juvenile steelhead carrying capacity. The density value of 5.5 fish/m2 used in the model was slightly lower than maximum values observed in similar studies (Table 7-2). We selected the lower value of 5.5 fish/m2 (from Meyer and Griffith 1997) to generate conservative estimates of winter carrying capacity because indications were that summer habitat was limiting. As discussed in Section 2.2.2, we consider habitat dominated by coarse, open framework substrate (i.e., cobble and boulder with minimal embedding finer substrate) to be high quality winter steelhead habitat. Each of the studies considered as sources for winter steelhead density data (Meyer and Griffith 1997, Bjornn et al. 1997, Redwood Sciences Lab and Stillwater Sciences, unpubl. data) were conducted using treatments with coarse substrates similar to those present in the SY, MY, and NY sub- basins.

February 2012 Stillwater Sciences 58 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table 7-2. Winter rearing densities reported for juvenile steelhead. Density Data location Source Notes (fish/m2) Mean density of juvenile steelhead (mean total Henrys Fork length of 96 mm; range of 52-155 mma) Meyer and Griffith of the Snake 5.5 remaining in winter instream experiments (1997) River, Idaho using wire-mesh enclosures with touching cobble and boulder substrate. Density of juvenile steelhead (mean fork Redwood Sciences length 120 mma) remaining in artificial stream Laboratory Lab and Stillwater channel with top layer of unembedded coarse 8.0 stream Sciences, unpubl. substrate (D50 128–180 mm) and bottom layer data of fully embedded coarse substrate after exposure to high water velocities. Mean densities of juvenile steelhead (mean total lengths of 106 mm, 116 mm and Hayden Creek, Bjornn et al. (1977) 7.5 119 mma) remaining in three artificial stream Idaho channels with unembedded cobble substrate after experimental winter trials. a Based on fish length and scale analysis of steelhead in Lagunitas Creek and tributaries (Marin County, California; Ettlinger et al. 2006) and tributaries to the Napa River (Napa County, California; Stillwater Sciences 2007b), we consider steelhead greater than about 100 mm to be in their second year of life (i.e., age 1+).

Usable fraction parameter values, calculated based on observed substrate composition in modeled sub-basins, were used in the HAB module to reflect the influence of habitat quality on winter carrying capacity. Dominant and subdominant substrate data collected for each mainstem habitat in the South and Middle Yuba rivers as part of the UYRSP rearing habitat assessment were used for the SY, MY, and NY model runs (Stillwater Sciences 2006a). Based on evidence from median substrate size (D50) data collected in the North Yuba River (Appendix E), we assumed that winter habitat quality in the NY sub-basin was as high or higher than that observed in the SY and MY sub-basins. For the NBB model run, we used dominant and subdominant substrate data collected during habitat mapping of the NBB sub-basin as part of Yuba County Water Agency Hydroelectric Project relicensing studies (K. Peacock, DTA/HDR, Bellingham, Washington, unpubl. data provided 1 December 2010). Appendix H, Tables H-4 through H-6 show winter juvenile rearing usable fraction parameter values used for each model run and provides a more detailed explanation of the methodology for calculating them.

7.2.1.5 Physical habitat thresholds As described in Section 6.2.1.5, physical thresholds can be used in the HAB module to identify channel reaches suitable for holding, spawning, and rearing and exclude all other reaches. In the upper Yuba River watershed RIPPLE model, the upstream distributions of steelhead spawning and rearing were restricted by either minimum channel width thresholds or channel gradient thresholds (Section 4). The locations of the downstream-most distribution of each life stage were determined by water temperature criteria (Section 4). However, these locations were implemented in the HAB module by choosing maximum channel width thresholds for each life stage that correspond to the downstream limit of suitable temperatures.

February 2012 Stillwater Sciences 59 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

7.2.1.6 Parameterization of Alternative Management Scenarios As described in Section 4, predicted increases in the amount of potentially suitable habitat under Alternative Management Scenarios 1 and 2 were reflected in the RIPPLE model by adjusting the downstream extent of thermally suitable mainstem channel habitat in the SY, MY, and NBB sub- basins, and by adjusting the amount of suitable spawning gravel in the NBB sub-basin. The model parameters that were changed to implement these habitat increases in the steelhead HAB module under Alternative Management Scenarios 1 and 2 are summarized in Table 7-3.

Table 7-3. Parameters changed in the HAB module for steelhead model runs for Alternative Management Scenarios 1 and 2 relative to current conditions. All other parameters were unchanged between scenarios. Sub- Alternative Management Alternative Management Parameters changed basins Scenario 1 Scenario 2 Spawning usable Increased to 50% of SY and Increased to match SY and NBB fraction MY values MY values Increased to allow use of Increased to allow use of Maximum channel thermally suitable channels thermally suitable channels width thresholds for MY further downstream than further downstream than spawning and rearing current conditions Scenario 1 No change in parameters Increased to allow use of Maximum channel (Scenario 1 parameters thermally suitable channels width thresholds for SY resulted in thermally suitable further downstream than spawning and rearing channels for the entire current conditions mainstem SY)

7.2.2 Results and discussion 7.2.2.1 Predicted distribution of suitable habitat As described in Section 4, the downstream extent of suitable steelhead spawning and summer rearing habitat for each scenario was initially defined by a 20°C MWAT thermal suitability water temperature criterion. It was assumed for modeling purposes that all portions of the channel network downstream of the natural passage barrier (in the mainstem) and the location of channel width and/or gradient thresholds (in the tributaries) would be suitable and accessible winter rearing habitat for steelhead under all scenarios and basins.

Suitable habitat for steelhead spawning and summer rearing in the SY sub-basin under current conditions was predicted to include 0.3 miles of the mainstem South Yuba River and 15.9 miles of tributary habitat (Map 5, Table 4-4, Figure 4-2). Suitable tributary habitat includes 3.3 miles of Canyon Creek, 6.6 miles of Poorman Creek, 0.5 miles of Humbug Creek, and 5.4 miles of habitat in the lower reaches of other tributaries. Based on available data, it was assumed for modeling purposes that water temperatures in all tributaries in the SY and other sub-basins are suitable for steelhead spawning and rearing.

Under Alternative Management Scenario 1, an additional 10.7 miles of the mainstem South Yuba River was predicted to be suitable for steelhead spawning and summer rearing, for a total of 11.0 miles of mainstem habitat. Under Alternative Management Scenario 2, an additional 11.8 miles of suitable steelhead habitat would be available in the mainstem South Yuba River compared with Scenario 1, for a total of 22.8 miles of mainstem habitat. Suitable tributary habitat predicted under the alternative management scenarios was the same as under current conditions. The upstream

February 2012 Stillwater Sciences 60 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed extent of tributary habitat in the SY sub-basin, as in all sub-basins modeled for steelhead, was restricted by channel width and/or gradient.

In the MY sub-basin 7.5 miles of the mainstem Middle Yuba River and 11.5 miles of tributary habitat was predicted to be suitable habitat for steelhead spawning and summer rearing under current conditions (Map 5, Table 4-4, Figure 4-2). Middle Yuba River tributaries predicted to have suitable steelhead habitat under current conditions include Wolf Creek (1.6 miles) and Oregon Creek (7.3 miles).

Under Alternative Management Scenario 1, an additional 6.7 miles of the mainstem Middle Yuba River was predicted to be suitable for steelhead spawning and summer rearing compared with current conditions, for a total of 14.2 miles of mainstem habitat. Under Alternative Management Scenario 2, an additional 11.7 miles of suitable steelhead habitat would be available in the mainstem Middle Yuba River compared with Scenario 1, for a total of 25.9 miles. As with the SY sub-basin, suitable tributary habitat predicted under the alternative management scenarios was the same as under current conditions.

In the NY sub-basin, 34.7 miles of the mainstem North Yuba River and 43.5 miles of tributary habitat was predicted to be suitable habitat for steelhead spawning and summer rearing under current conditions (Map 5, Table 4-4, Figure 4-2). Suitable tributary habitat was predicted to include 4.3 miles of Slate Creek, 8.8 miles of Canyon Creek, 2.9 miles of Goodyears Creek, 6.9 miles of the Downie River, 6.7 miles of Lavezzola Creek, 2.6 miles of Jim Crow Creek, 1.3 miles of Haypress Creek, and 10 miles of habitat in other tributaries. As discussed above, the upstream extent of tributary habitat—for both summer and winter rearing—was restricted by channel width and/or gradient. Alternative management scenarios were not modeled in the NY sub-basin.

In the NBB sub-basin, suitable summer rearing habitat for steelhead under current conditions was predicted to include 1.7 miles of the mainstem North Yuba River (from New Bullards Bar Dam downstream to NY RM 0.63, just upstream of the Middle Yuba River confluence), 2 miles of the mainstem Yuba River downstream of New Colgate Powerhouse, and 0.6 miles of lower Dobbins Creek (Map 5, Table 4-4, Figure 4-2). The Yuba River downstream of New Colgate Powerhouse and the lower 0.6 miles of Dobbins Creek were also predicted to have suitable steelhead spawning habitat under current conditions. However, due to lack of suitable spawning gravel (Nikirk and Mesick 2006), no spawning habitat was assigned to the 2.2 miles between New Bullards Bar Dam and the Middle Yuba River confluence. Suitable winter rearing habitat in the NBB sub-basin was assumed to be present under all scenarios in the entire mainstem channel and in Dobbins Creek upstream to the location of the channel width and/or gradient threshold, as described in Section 4.2. Under Alternative Management Scenarios 1 and 2, the entire 10.3 miles of mainstem channel from New Bullards Bar Dam downstream to Englebright Reservoir (Rice’s Crossing), and the lowermost 0.6 miles of Dobbins Creek, were predicted to be suitable for steelhead spawning and summer rearing. The increased extent of suitable mainstem summer rearing habitat under the alternative management scenarios would result from increased cold water releases from New Bullards Bar Dam. The increased extent of mainstem spawning habitat would result from gravel augmentation that would occur under each scenario. As described previously, gravel augmentation under Scenario 1 would be approximately equivalent to 50% of its unimpaired extent, and under Scenario 2 would be approximately equal to its unimpaired extent.

February 2012 Stillwater Sciences 61 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Expanded steelhead distribution Applying the higher thermal suitability criteria in the SY and MY sub-basins to expand the lower mainstem distribution of steelhead summer rearing and spawning resulted in substantially more habitat compared with the 20°C temperature criterion (Table 4-5, Maps 5 and 6). In the mainstem South Yuba River the higher criterion (25.2°C) resulted in 17.3 more miles of summer rearing habitat under current conditions compared with the lower, more conservative criterion (20°C). Applying the higher criterion under Scenarios 1 and 2 resulted in an additional 24.7 miles and 12.9 miles, respectively of summer rearing habitat in the mainstem South Yuba River (Table 4-5, Maps 5 and 6).

In the mainstem Middle Yuba River, use of the higher water temperature criterion (23.2°C) to expand downstream distribution resulted in an additional 10.4 miles of summer rearing habitat under current conditions compared with the 20°C temperature criterion. Applying the higher criterion under Scenarios 1 and 2 resulted in 9.2 more miles of summer rearing habitat in the mainstem Middle Yuba River under both scenarios (Table 4-5, Maps 5 and 6).

7.2.2.2 Carrying capacity estimates Results of the RIPPLE HAB module indicate that, for each model sub-basin and scenario, assuming sufficient adult spawning escapement, there was ample spawning habitat (redd carrying capacity) to fully seed the thermally suitable age 1+ juvenile summer rearing habitat (Table 7-4). This conclusion also assumes moderate survival during the embryo incubation period and during the summer and winter of the first year of juvenile rearing. Gravel permeability measurements in the Middle Yuba and South Yuba rivers predict relatively high embryo survival and availability summer and winter cover, off-channel habitats, and preferred substrate suggest relatively high age-0 rearing survival (UYRSPST 2007). The substantially higher redd carrying capacity predicted for the NY sub-basin (Figure 7-1) is due to a greater length and area of thermally suitable mainstem channel and the presence of extensive tributary habitat relative to other sub- basins (see Table 4-4).

Table 7-4. RIPPLE-predicted habitat carrying capacities for steelhead life stages for each modeled reach and scenario in the upper Yuba River watershed.1

Carrying South Middle North capacity Scenario2 NBB Yuba Yuba Yuba,3 (K) CC 393 1,503 15,626 121 Redds S1 2,333 2,613 n/a 1,884 S2 4,826 4,864 n/a 3,770 CC 8,202 17,077 212,643 19,406 Summer 1+ S1 43,659 35,478 n/a 67,411 S2 96,256 72,166 n/a 67,411 CC 4,198,783 3,037,187 6,485,401 2,689,157 Winter 1+ S1 4,198,783 3,037,187 n/a 2,689,157 S2 4,198,783 3,037,187 n/a 2,689,157 1 Carrying capacities represent estimates derived using a 20°C thermal suitability criterion for summer rearing. 2 CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2. 3 Alternative management scenarios were not simulated for the North Yuba sub-basin.

February 2012 Stillwater Sciences 62 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

16,000

14,000 CC S1 S2 12,000

10,000 redds

of 8,000

Number 6,000

4,000

2,000

0 South Yuba Middle Yuba North Yuba NBB

Figure 7-1. Number of steelhead redds predicted under current conditions and two modeled scenarios. Alternative management scenarios were not modeled for the North Yuba sub-basin. CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2.

Notably, HAB module results also indicate that age 1+ summer steelhead habitat is considerably more limiting than winter habitat. Under current conditions, predicted age 1+ winter habitat capacity ranged from 30 times higher than summer rearing habitat capacity in the NY sub-basin to 512 times higher in the SY sub-basin (Table 7-4). These results indicate that the quantity of summer habitat will likely limit the potential size of the steelhead population in upper Yuba River watershed. The pronounced summer rearing habitat limitations apparent in the SY and MY sub- basin for all scenarios and the NBB sub-basin under current conditions are, in part, attributable to the additional extent of channel that is thermally suitable in the winter as compared with the summer (Map 5). Even in model runs where summer habitat was predicted to be thermally suitable in the entire mainstem study reach (NY sub-basin and NBB sub-basin under Alternative Management Scenarios 1 and 2), summer habitat is still limiting due to the larger area of channel inundated during winter flows. The relatively high summer juvenile carrying capacity predicted for the shorter NBB sub-basin compared to the MY and SY sub-basins under Alternative Management Scenarios 1 and 2 can be attributed to the significantly wider summer low channel, which resulted in a greater area of rearing habitat. Lastly, higher winter rearing densities are possible since cold water temperature decreases territoriality, causing fish to spend much of their time hiding in protected micro-sites associated with unembedded cobble and boulder substrates, which is reflected in the densities used in the model. These substrates are relatively plentiful in the upper Yuba River watershed (Appendix H, Table H-5). Preliminary model gaming suggests

February 2012 Stillwater Sciences 63 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed that winter density and/or usable fraction parameters would need to be reduced substantially before winter habitat becomes limiting. Differences in smolt production between scenarios and sub-basins are discussed further in Section 7.3 below.

Comparison of carrying capacities using 20°C and expanded distribution Table 7-5 compares carrying capacities predicted for each life stage in the SY and MY sub-basins using the 20°C criterion to define downstream distribution to carrying capacities predicted based on observed O. mykiss distributions and water temperatures measured at those locations (25.2°C and 23.2°C for the SY and MY, respectively). These results can be viewed as the likely lower and upper bounds of the range of carrying capacities for the SY and MY sub-basins.

Table 7-5. Comparison of predicted habitat carrying capacities for steelhead life stages using 20°C and higher water temperature criteria to define extent of suitable habitat.

Carrying South Yuba Middle Yuba capacity Scenario1 (K) 20°C 25.2°C 20°C 23.2°C criterion criterion criterion criterion CC 393 3,745 1,503 3,284 Redds S1 2,333 6,996 2,613 4,349 S2 4,826 6,996 4,864 6,761 CC 8,202 53,529 17,077 36,227 Summer 1+ S1 43,659 125,394 35,478 58,470 S2 96,256 142,594 72,166 99,430 CC 4,198,783 4,198,783 3,037,187 3,037,187 Winter 1+ S1 4,198,783 4,198,783 3,037,187 3,037,187 S2 4,198,783 4,198,783 3,037,187 3,037,187 1 CC = current conditions, S1 = Alternative Management Scenario 1, and S2 = Alternative Management Scenario 2.

For all scenarios in both the SY and MY sub-basins, the expanded habitat distribution based on the higher temperature criteria resulted in substantially more redds and age 1+ summer rearing habitat compared with the 20°C temperature criterion. There was no difference in the amount of winter habitat capacity, since the entire length of the mainstem channels was thermally suitable in the winter, regardless of scenario or which criterion was applied.

In the SY sub-basin under current conditions, the number of steelhead redds predicted using the 25.2°C temperature criterion was approximately 10 times higher than the more conservative estimate using the 20°C temperature criterion. For Scenario 1, redd carrying capacity was predicted to be three times higher when applying the 25.2°C criterion, but only about 1.5 times higher for Scenario 2. Predicted carrying capacity of age 1+ summer rearing habitat based on the 25.2°C criterion was about 6.5 times higher under current conditions, 2.9 times higher for Scenario 1, and 1.4 times higher for Scenario 2.

In the MY sub-basin under current conditions, the predicted number of steelhead redds based on the 23.2°C temperature criterion was about twice as high as under the more conservative 20°C temperature criterion. For Scenario 1, redd carrying capacity predicted by applying the 23.2°C criterion was predicted to be 1.7 times higher than that predicted using the 20°C criterion, but

February 2012 Stillwater Sciences 64 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed only about 1.4 times higher for Scenario 2. Predicted carrying capacity for age 1+ summer rearing habitat based on the 23.2C criterion was about 2.1 times higher under current conditions, 1.6 times higher for Scenario 1, and 1.4 times higher for Scenario 2.

These results indicate that distribution of summer rearing habitat in the lower mainstems is a key driver of steelhead smolt production in the upper Yuba River watershed. The model output is clearly sensitive to the amount of suitable summer rearing habitat, as defined primarily by water temperature and the application of life stage-specific suitability criteria. The potential downstream extent of thermally suitable steelhead habitat in the upper Yuba River watershed is a key model uncertainty.

7.3 Smolt Production Estimates 7.3.1 Methods We estimated potential steelhead smolt production based on carrying capacities predicted for age 1+ juveniles in the summer. Summer 1+ carrying capacity estimates from the HAB module were multiplied by summer and winter density-independent survival (e.g., predation and disease) estimates of 90% for each life stage (resulting in a total survival of 81% from summer until smolt emigration). Available evidence suggests that once steelhead survive their first year, their survival during the second summer and winter is very high. In a study in Upper Penitencia Creek and Arroyo Aguague, Santa Clara County, California, spring and fall population estimates for age 1+ and older steelhead were not significantly different (Stillwater Sciences 2006d). A similar study from Lagunitas Creek found that the abundance of age 1+ steelhead remained approximately the same from November until February (Stillwater Sciences 2008). Both of these studies suggest very high survival, approaching 100%. We used conservatively low survival estimates of 90% for both summer and winter, assuming that predation and other potential stressors in the larger upper Yuba River watershed branches are likely higher than smaller, coastal river systems such as Lagunitas and Upper Penitencia creeks. In comparison Lestelle et al. (2004) assumed that survival of juvenile steelhead in both summer and winter periods was 85% for their Ecosystem Diagnosis and Treatment model.

Smolt production estimates assume that summer 1+ habitat was fully seeded, that is, sufficient adults will return from the ocean to produce enough eggs to survive incubation and fry to survive through the first summer and winter before fully seeding age 1+ summer habitat. As described in Section 7.2.2, the HAB module predictions of redd carrying capacity suggests that there is ample spawning habitat to produce enough fry to survive to fully seed age 1+ summer rearing habitat.

7.3.2 Results and discussion Table 7-6 shows estimated numbers of steelhead smolts produced in each upper Yuba River watershed sub-basin and scenario modeled. In the SY sub-basin, estimated steelhead smolt production potential under Alternative Management Scenarios 1 and 2 and using the 20°C temperature criterion was approximately 5 and 12 times higher, respectively, than current conditions. In the MY sub-basin, smolt production potential was about 2 and 4 times higher under Alternative Management Scenarios 1 and 2, respectively, than under current conditions using the 20°C temperature criterion. Differences in smolt production estimates between the conservative (20°C criterion used to define habitat distribution) and expanded (25.2°C and 23.2°C criteria in the SY and MY sub-basins, respectively) distributions (Table 7-6) are proportional to differences in age 1+ summer rearing capacity (Tables 7-5), and further underscore the sensitivity of the model to water temperature and the extent of available habitat in the lower mainstem channels of

February 2012 Stillwater Sciences 65 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed the South Yuba and Middle Yuba rivers. Under the higher temperature criteria in the SY and MY sub-basins, the increase in estimated smolt production between Alternative Management Scenario 1 and Alternative Management Scenario 2 is smaller than the increase between current conditions and Scenario 1. This is because the majority of accessible habitat that is thermally unsuitable under current conditions would become thermally suitable under Alternative Management Scenario 1. Therefore, the remaining increase in thermally suitable habitat provided under Alternative Management Scenario 2 would be relatively small.

In the NBB sub-basin, estimated smolt production was 3.5 times higher under both alternative management scenarios compared with current conditions. These increases are driven in part by the increased length of mainstem channels that become thermally suitable (Map 5) and in part by the increased rearing area resulting from increased summer low flow widths under the alternative management scenarios.

Table 7-6. Steelhead smolt production estimates based on RIPPLE-predicted summer carrying capacities for age 1+ steelhead for each modeled sub-basin and scenario in the upper Yuba River watershed.

SY sub-basin MY sub-basin NY sub- NBB sub- Scenario 20°C 25.2°C 20°C 23.2°C basin1 basin criterion criterion criterion criterion CC 6,644 43,358 13,832 29,344 172,241 15,719 S1 35,364 101,569 28,737 47,361 n/a 54,603 S2 77,967 115,501 58,454 80,538 n/a 54,603 1 Alternative management scenarios were not simulated for the NY sub-basin.

There was no increase in smolt production in the NBB sub-basin between Alternative Management Scenarios 1 and 2—despite the doubling of spawning habitat simulated by Scenario 2 and resultant doubling of redd carrying capacity (Table 7-3). This is because summer age 1+ rearing habitat, which was more limiting than spawning habitat, did not increase between scenarios.

The RIPPLE model results further suggest that the NY sub-basin has the potential to produce substantially more steelhead than the SY and MY sub-basins, regardless of the temperature criteria used to restrict distribution. The NY sub-basin (under current conditions) was predicted to produce 1.5 and 2.1 times more steelhead smolts than the SY and MY sub-basins, respectively, under Alternative Management Scenario 2—even when the higher temperature criteria were used to expand the potential steelhead distribution in the SY and MY sub-basins (Table 7-6). The greater smolt production in the NY sub-basin is due not only to the larger channel size and much greater extent of accessible tributary habitat (Table 4-4), but also to differences in habitat type composition. The NY sub-basin has a higher frequency of riffles (Appendix E, and Stillwater Sciences 2006b), which typically support relatively higher age 1+ densities than pools in larger, lower gradient channels (Gast et al. 2005).

In summary, several factors point to the upper Yuba River watershed, particularly the NY sub- basin, as having excellent potential for sustaining healthy steelhead populations. An abundance of high quality rearing habitat currently supports relatively high densities of resident rainbow trout in reaches with suitable summer water temperatures (NID and PG&E 2009). Conditions for juvenile steelhead rearing in the upper Yuba River watershed are currently good, but as

February 2012 Stillwater Sciences 66 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed demonstrated by the model, alternative management to reduce summer water temperatures would greatly increase smolt production in the SY, MY, and NBB sub-basins.

7.4 Steelhead—Model Sensitivity and Uncertainty As described in Section 6.3, the level of importance of model uncertainties depends on the degree of model sensitivity, as well as the project objectives. In the model development for this study, we focused our assessment of model sensitivity on parameter values likely to change model results. Parameters with a low level of certainty and high level of sensitivity were recommended for additional sampling. As described in Section 8, systematic model gaming, validation, and refinement are recommended to enhance model predictions. The following are some of the key uncertainties in potentially sensitive model parameters for the steelhead RIPPLE model:  Summer rearing density values strongly influence the model results and have a high degree of uncertainty. As such, age-1+ summer habitat capacity is a key model parameter that warrants further analysis.  The proportion of resident versus anadromous trout is a model uncertainty that has yet to be investigated. We ran the RIPPLE steelhead model assuming the migratory life history would pre-dominate. However, the fraction of the population comprised of resident rainbow trout will likely vary between basins depending on water temperatures, stream flows, predation pressures and productivity (Zimmerman et al. 2009, Mitchell 2010). If the resident component was substantial the effective summer carrying capacity for age 1+ juvenile steelhead would be lower than our predictions and thus our estimates of smolt production would be too high.  As discussed in Section 4 of this study, all tributaries were not evaluated for thermal suitability or flow (such as Kentucky Ravine at confluence with the South Yuba River); therefore it is possible that the model overestimates habitat capacity. However, the overall contribution to carrying capacity and production from these relatively short accessible tributary reaches is expected to be quite low relative to basin-wide capacity and production. Furthermore tributary production does not change between scenarios, thereby avoiding any bias in comparing future alternative conditions.  The extent of spawning distribution due to thermal suitability for spawning/incubation is a model uncertainty. However, it is clear that summer rearing limits smolt production and thus spawning distribution is not a sensitive model parameter as long as juvenile habitat is fully seeded  Juvenile mortality due to predation in Englebright Reservoir and the lower reaches of each sub-basin is currently not included in the model predictions. We recommend additional study to further explore the potential effects of predation on steelhead survival and production.  Trout and pikeminnow abundance in the Upper Yuba River watershed likely varies between the branches and will affect juvenile steelhead carrying capacity to an uncertain extent.

8 MODEL CONSIDERATIONS

The RIPPLE model application for the upper Yuba River watershed is best suited to explore watershed-scale population dynamics, habitat capacity and productivity, species-specific limiting conditions and the relative benefits of various management alternatives. Each of these elements is

February 2012 Stillwater Sciences 67 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed an important consideration for reintroduction potential in the upper Yuba River watershed—the driving objective behind this study. As with any model, it is essential to understand the intended purpose of the mathematical simulations, the data sources employed, and the potential constraints of the model. The introduction in Section 1 describes the purpose of the study, Sections 4 through 7 present methods and results, and Sections 6 and 7 provide a focused account of parameter uncertainty and sensitivity. This section provides an overview of model challenges and opportunities for validation and model refinement.

8.1 Modeling Challenges The following factors created challenges in the development of the upper Yuba River habitat capacity and population dynamics model:  The absence of anadromous fish in the upper Yuba River watershed required model assumptions regarding various parameters. Assumptions were based on the best available data and in some cases, professional judgment. The proportion of the spring-run Chinook salmon population attributed to different life history strategies (e.g., “efry”, stream type or ocean type) is an assumption that would benefit from validation and refinement of input parameters.  Downstream (i.e., lower river, estuary, ocean) survival of spring-run Chinook salmon and steelhead. These largely unknown parameters will be simulated by additional modeling downstream of Englebright Dam.  The general challenge of using data collected for other purposes, which does not always closely match ideal model requirements.  Limited spatial and temporal extent of water temperature data. This is particularly concerning given the strong influence of temperature on habitat suitability for reintroduced salmon and steelhead in the upper Yuba River watershed  The limited availability of data in the North Yuba River sub-basin (e.g., trout density and distribution, habitat type frequency, long-term water temperature).  The confounding effect of natural environmental variability on the accuracy of model parameters such as temperature and flow. In order to reduce this variability, long term data sets are preferable, but typically unavailable.

Our approach to these challenges was to present a transparent, well documented model that details data sources, methods, results and uncertainties. We anticipate that the findings of this effort will be useful to resource agencies and stakeholders to evaluate management alternatives and the potential benefits of additional study.

8.2 Model Validation The accuracy of model assumptions and results are best demonstrated by field validation. The following model predictions and assumptions are recommended priorities for validation:  Channel geometry in the Middle Yuba and South Yuba rivers (bankfull width and depth and winter base flow width and depth).  Channel geometry, habitat type frequency, and substrate composition in the North Yuba River and Yuba River between New Bullards Bar Dam and Englebright Reservoir.  Habitat type frequency in the North Yuba River.  Habitat type frequency in the major tributaries of the Middle Yuba and South Yuba rivers

February 2012 Stillwater Sciences 68 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

 Resident trout density and distribution in the North Yuba River upstream of New Bullards Bar Reservoir and between New Bullards Bar Dam and Englebright Reservoir.

In some cases validation is recommended for data that was explicitly collected as part of this study (e.g., North Yuba River habitat type frequency). Although such samples were designed to represent the range of conditions found in the sub-basin, the spatial extent of areas such as the North Yuba is large relative to the sample size. Field validation in these cases would confirm the accuracy of parameter assumptions.

8.3 Recommendations for Model Refinement Considerable efforts were made to obtain the best available data with which to parameterize the RIPPLE model. Resulting model outputs have been carefully documented, subject to technical review, compared with regionally applicable data and are worthy of scientific scrutiny. Nevertheless, we recognize models can always be refined with input from knowledgeable experts, field validation and the collection of additional information.

The following studies are suggested for future model advancement:  Refine estimates of spawning gravel area and usable fraction in the NY sub-basin.  Refine habitat type-specific density estimates of O. mykiss in the upper Yuba River watershed to increase spatial extent of samples and investigate possible differences in between the NY and other sub-basins  Conduct a literature review to provide estimates of trap and truck mortality associated with the specific operations proposed for fish passage in the upper Yuba River watershed. Refine outmigrant survival estimates accordingly.  Expand the RIPPLE model to fully simulate upper Yuba River steelhead population dynamics.

In the event that pilot or large-scale reintroduction efforts occur, focused studies of salmon and steelhead population dynamics and habitat use are recommended to refine model predictions. Such additional study is prudent given the model structure provides valuable simulation capabilities for management alternatives that would otherwise take years to implement and monitor. The following studies would provide data specific to the upper Yuba River watershed to reduce model uncertainty and confirm key parameter assumptions:  Collect habitat type-specific juvenile spring-run Chinook salmon and steelhead density data in tributary and mainstem channels in each sub-basin.  Conduct outmigrant trapping on the mainstem South Yuba, Middle Yuba, and North Yuba rivers to enumerate juveniles and provide size/age data.  Conduct abundance surveys (e.g., mark-recapture studies) in spring and late fall to estimate spring-run Chinook salmon and steelhead summer survival.  Evaluate the potential bias caused by using rainbow trout juvenile rearing density as a surrogate to parameterize steelhead carrying capacity.

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NID and PG&E (Nevada Irrigation District and Pacific Gas and Electric Company). 2009. Stream fish populations. 2008 Progress Report. Technical Memorandum 3-1. Prepared by NID, Grass Valley, California, and PG&E, San Francisco, California.

NID and PG&E (Nevada Irrigation District and Pacific Gas and Electric Company). 2011. Application for new license major project-existing dam, Volume II: Exhibit E. Yuba-Bear Hydroelectric Project (FERC Project No. 2266-096). Drum-Spaulding Project (FERC Project No. 2310-173). Prepared by NID, Grass Valley, California and PG&E, San Francisco, California.

Nicholas, J. W., and D. G. Hankin. 1989. Chinook salmon populations in Oregon coastal river basins: descriptions of life histories and assessment of recent trends in run strengths. Report EM 8402. Oregon Department of Fish and Wildlife, Research and Development Section, Corvallis.

Nikirk, N., and C. Mesick. 2006. Spawning habitat evaluation. Prepared by CH2M Hill, Sacramento, California and U.S. Fish and Wildlife Service, Sacramento, California for Upper Yuba River Studies Program Study Team, Sacramento, California. Appendix D in Upper Yuba River watershed Chinook salmon and steelhead habitat assessment. Technical Report. Prepared by UYRSPST for California Department of Water Resources, Sacramento, California.

NOAA (National Oceanic and Atmospheric Administration). 2002. Biological opinion on interim operations of the CVP and SWP between April 2000 and March 2004 on federally listed

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Petrosky, C. E. 1990. Estimating spring Chinook parr and smolt abundance in wild and natural production areas. Pages 57–61 in D. Parker, editor. Status and future of spring Chinook salmon in the Columbia River basin—conservation and enhancement. National Marine Fisheries Services' spring Chinook salmon workhop, 8–9 November 1989.

Reedy, G. D. 1995. Summer abundance and distribution of juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) in the Middle Fork Smith River, California. Master's thesis. Humboldt State University, Arcata, California.

Reedy, G. 2009. Unpublished water temperature data from the North Yuba River sub-basin. Collected by the South Yuba River Citizens League. Provided to Stillwater Sciences in December, 2009.

Reisenbichler, R. R., J. D. McIntyre, and R. J. Hallock. 1982. Relation between size of Chinook salmon, Oncorhynchus tshawytscha, released at hatcheries and returns to hatcheries and ocean fisheries. California Fish and Game 68: 57–59.

Reynolds, F. L., T. J. Mills, R. Benthin, and A. Low. 1993. Restoring Central Valley streams: a plan for action. California Department of Fish and Game, Inland Fisheries Division, Sacramento.

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Stillwater Sciences. 2006b Upper Yuba River Chinook salmon and steelhead rearing habitat assessment. Technical Appendix. Prepared by Stillwater Sciences, Berkeley, California for CH2M Hill, Sacramento, California. Appendix E in Upper Yuba River watershed Chinook salmon and steelhead habitat assessment. Technical Report. Prepared by UYRSPST for California Department of Water Resources, Sacramento, California.

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R.L. Brown, editor. Contributions to the biology of Central Valley salmonids. California Department of Fish and Game Bulletin 179.

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Maps

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in the Upper Yuba River Watershed Watershed Yuba River in the Upper

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

Modeled sub-basins of the upper Yuba River watershed. Yuba River watershed. of the upper Modeled sub-basins

Technical Report Technical Map 1. February 2012

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in the Upper Yuba River Watershed Watershed Yuba River in the Upper

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

s for channels in the upper Yuba River watershed. upper Yuba River watershed. for channels in the s

Technical Report Technical area Map 2. Contributing drainage February 2012

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in the Upper Yuba River Watershed Watershed Yuba River in the Upper

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

Channel gradients in the upper Yuba River watershed. in the upper Yuba River watershed. Channel gradients

Technical Report Technical Map 3. February 2012

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in the Upper Yuba River Watershed Watershed Yuba River in the Upper

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run rrent conditions and Alternative Management Scenarios 1 and 2. 1 and Scenarios Management Alternative and rrent conditions

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Technical Report Technical spri for habitat rearing summer holding and Map 4. Extent of predicted February 2012

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in the Upper Yuba River Watershed Watershed Yuba River in the Upper

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run ios 1 and 2, using a 20°C water temperature criterion to define to define criterion temperature water a 20°C 2, using 1 and ios s and Alternative Management Scenar s and Alternative

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Technical Report Technical for st habitat and summer rearing spawning Map 5. Extent of predicted February 2012

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in the Upper Yuba River Watershed Watershed Yuba River in the Upper

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run enarios 1 and 2, using 25.2°C and 23.2°C water temperature temperature water 23.2°C and 25.2°C 2, using 1 and enarios s and Alternative Management Sc s and Alternative

eelhead in the upper Yuba River watershed under current condition watershed under eelhead in the upper Yuba River h Yuba and Middle Yuba sub-basins, respectively. respectively. h Yuba and Middle sub-basins,

criteria to define suitable habitat in the Sout habitat suitable define to criteria

Technical Report Technical for st habitat and summer rearing spawning Map 6. Extent of predicted February 2012

Appendices

Appendix A

Meteorological and Streamflow Conditions Compared to Historical Averages

Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

INTRODUCTION

This appendix provides historical meteorological context in which stream temperature measurements were made. Inter-annual variation of stream temperature is determined by an interaction between climatic variables (shortwave/longwave radiation, air temperature, cloud cover, etc.), and hydrology (hyporheic groundwater contribution, snowmelt timing/magnitude, etc.). Stream temperature is a direct reflection of the unique interaction of these variables during the time period of interest. Two of the main factors that account for the inter-annual variability in stream temperatures are air temperature and streamflow.

Monthly air temperature data were obtained from the Western Regional Climate Center (http://www.wrcc.dri.edu/cgi-bin/cliMAIN.pl?ca0897) for the Blue Canyon, California weather station. This station was selected because of its long period of record and proximity to the South and Middle Yuba rivers. Data was also obtained from the Downieville, California weather station (http://www.wrcc.dri.edu/cgi-bin/cliMAIN.pl?ca2500) for its proximity to the North Yuba River. Streamflow data were obtained from the USGS for each river basin; generally the gages are located downstream form where water temperatures were measured.

AIR TEMPERATURE

Table A-1. Average monthly air temperatures (°F) at Blue Canyon, CA compared to the long- term average. Period of record is 1944-2010. Years and months were not used for annual or monthly statistics if more than 5 days are missing from the record. Data obtained from the Western Regional Climate Center, 2011.

Period of record Jun Jul Aug Sep Oct Jul–Aug (avg.) Jun–Sept (avg.) Mean °F (1944–2010) 60.50 68.53 67.66 63.11 53.99 68.12 64.98 2003 64.80 72.97 66.94 68.90 61.06 69.96 68.40 2004 63.13 69.53 68.95 62.73 49.81 69.24 66.09 2005 54.88 72.40 70.40 59.62 52.81 71.40 64.33 2006 66.30 73.47 68.65 65.27 53.50 71.06 68.42 2007 63.08 71.13 70.65 60.27 50.60 70.89 66.28 2008 64.75 71.89 71.89 68.08 57.00 71.89 69.15 2009 60.22 72.56 69.42 68.57 51.89 70.99 67.69 2010 60.35 70.87 67.23 65.40 54.06 69.05 65.96

February 2012 Stillwater Sciences A-1 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table A-2. Percentile rankings of average monthly air temperatures at Blue Canyon, CA. Percentiles indicate the percentage of years which that month’s average air temperature exceeded. The period of record is 1944–2010. The years 2003–2010 had some of the warmest individual months on record. 2008 was the warmest summer on record. Data obtained from the Western Regional Climate Center, 2011.

Percentile ranking Jun Jul Aug Sep Oct Jul–Aug (avg.) Jun–Sep (avg.) 2003 Percentile 0.89 0.98 0.37 0.98 0.98 0.67 0.95 2004 Percentile 0.72 0.58 0.61 0.38 0.14 0.62 0.69 2005 Percentile 0.07 0.92 0.79 0.13 0.41 0.93 0.39 2006 Percentile 0.97 1.00 0.57 0.75 0.52 0.92 0.97 2007 Percentile 0.71 0.80 0.84 0.20 0.23 0.87 0.75 2008 Percentile 0.85 0.87 0.98 0.95 0.76 1.00 1.00 2009 Percentile 0.48 0.95 0.69 0.97 0.27 0.89 0.92 2010 Percentile 0.49 0.77 0.44 0.76 0.54 0.59 0.68

Table A-3. Average monthly air temperature at Downieville, CA. Long-term average compared with 2010 and percentile rankings of the summer of 2010. Data obtained from the Western Regional Climate Center, 2011.

Percentile Jun Jul Aug Sep Oct Annual Jul–Aug Jun–Sep Mean F (1911–2010) 63.05 69.05 67.75 62.71 54.42 52.65 68.43 65.69 2010 63.37 70.73 67.19 63.63 56.65 52.22 68.96 66.23 2010 Percentile 0.54 0.77 0.44 0.60 0.78 0.29 0.57 0.60

February 2012 Stillwater Sciences A-2 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

STREAMFLOW

South Yuba at Jones Bar (USGS Gage 11417500) Table A-4. Average monthly flow (cfs) 2003–2010 compared to the long-term average (1940– 2010) at the South Yuba River at Jones Bar. Data obtained from USGS, National Water Information System, 2011.

Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Mean cfs (1940–2010) 728 758 746 684 917 653 116 41 40 76 181 466 2003 487 289 412 705 1,233 807 84 68 55 53 77 383 2004 360 718 510 249 126 74 51 43 43 74 81 221 2005 465 379 825 568 2,125 1,192 113 54 45 50 70 1,880 2006 1,538 996 1,504 2,947 3,101 759 82 59 51 55 79 196 2007 146 501 355 204 149 74 44 38 40 60 57 129 2008 334 408 326 254 238 73 42 37 55 48 94 103 2009 187 597 758 291 1,700 120 34 35 36 69 66 130 2010 370 371 432 657 825 1,733 181 59 52

Table A-5. Median monthly flow (cfs) 1940–2010 and percentile rankings of monthly flow 2003– 2010. Percentiles indicate the percentage of years which that month’s average flow exceeded. Data obtained from USGS, National Water Information System, 2011.

Percentile ranking Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Median cfs (1940–2010) 401 533 574 485 535 391 61 42 41 52 99 231 2003 Percentile 0.56 0.21 0.24 0.66 0.69 0.73 0.71 0.95 0.85 0.54 0.35 0.73 2004 Percentile 0.46 0.61 0.38 0.19 0.12 0.22 0.42 0.53 0.53 0.81 0.42 0.49 2005 Percentile 0.54 0.32 0.72 0.55 0.88 0.83 0.80 0.73 0.58 0.40 0.30 0.95 2006 Percentile 0.88 0.74 0.90 1.00 0.98 0.66 0.69 0.83 0.69 0.58 0.39 0.46 2007 Percentile 0.18 0.44 0.19 0.10 0.17 0.24 0.34 0.41 0.46 0.61 0.16 0.30 2008 Percentile 0.44 0.37 0.16 0.21 0.31 0.17 0.29 0.37 0.83 0.37 0.47 0.19 2009 Percentile 0.25 0.53 0.64 0.26 0.81 0.34 0.15 0.34 0.37 0.74 0.23 0.32 2010 Percentile 0.49 0.30 0.29 0.64 0.61 0.92 0.90 0.80 0.73

February 2012 Stillwater Sciences A-3 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Middle Yuba above Our House Dam (USGS Gage 11408880 + USGS Gage 11408870) Table A-6. Average monthly flow (cfs) 2003–2010 compared to the long-term average (1940– 2010) at the Middle Yuba River above Our House Dam. Data obtained from USGS, National Water Information System, 2011.

Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Mean cfs (1988–2010) 492 471 594 573 643 283 83 41 35 42 75 261 2003 504 306 399 554 754 437 77 53 38 33 49 269 2004 241 440 492 379 261 86 42 30 29 56 57 133 2005 276 295 551 521 1,421 387 99 50 41 41 60 1,291 2006 986 852 905 2,099 1,800 247 86 52 42 42 68 187 2007 153 431 396 339 264 71 40 30 30 45 40 71 2008 183 262 363 385 402 106 38 28 27 77 70 60 2009 149 394 611 404 914 125 49 34 28 32 58 40 2010 209 263 338 543 568 482 101 50 36

Table A-7. Median monthly flow (cfs) 1988–2010 and percentile rankings of monthly flow 2003– 2010. Percentiles indicate the percentage of years which that month’s average flow exceeded. Data obtained from USGS, National Water Information System, 2011.

Percentile ranking Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Median cfs (1988–2010) 258 378 471 470 400 194 57 37 35 41 62 130 2003 Percentile 0.71 0.38 0.38 0.71 0.71 0.81 0.62 0.86 0.62 0.29 0.29 0.76 2004 Percentile 0.48 0.67 0.52 0.29 0.24 0.19 0.24 0.24 0.29 0.90 0.38 0.52 2005 Percentile 0.52 0.33 0.57 0.62 0.86 0.76 0.81 0.67 0.81 0.43 0.48 0.95 2006 Percentile 0.90 0.81 0.86 1.00 1.00 0.62 0.71 0.81 0.86 0.62 0.57 0.62 2007 Percentile 0.24 0.57 0.33 0.24 0.29 0.14 0.19 0.19 0.38 0.71 0.10 0.29 2008 Percentile 0.33 0.19 0.24 0.33 0.52 0.29 0.14 0.14 0.14 0.95 0.62 0.14 2009 Percentile 0.19 0.52 0.71 0.38 0.81 0.38 0.38 0.33 0.19 0.24 0.43 0.05 2010 Percentile 0.43 0.24 0.19 0.67 0.57 0.86 0.86 0.71 0.52

February 2012 Stillwater Sciences A-4 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

North Yuba below Goodyear’s Bar USGS Gage 11413000 Table A-8. Long-term (1931–2010) averages of mean and median monthly flow (cfs) compared to 2010 at the North Yuba River below Goodyear’s Bar. Percentiles indicate the percentage of years which that month’s average flow exceeded. Data obtained from USGS, National Water Information System, 2011.

Percentile Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Mean cfs (1931–2010) 859 935 1,063 1,366 1,809 1,095 365 185 150 181 334 643 Median cfs (1931–2010) 504 780 917 1,312 1,746 827 269 173 147 160 214 320 2010 395 463 686 1,129 1,616 2,112 447 199 154 2010 Percentile 0.44 0.30 0.32 0.42 0.55 0.82 0.77 0.65 0.55

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Appendix B

HFAM Water Temperature Model Output for the South Yuba and Middle Yuba Rivers

40 39 37 35.63 34.1 32.65

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Appendix C

2010 Water Temperature Data for the North Yuba River

Creek

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/

7

C Degrees Figure C-1. February 2012 Technical Report Technical Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table C-1. Water temperature logger location data. Source: NMFS (2010) unpublished data.

Name Hobo serial # Latitude Longitude Elevation N39 W121 Below_Canyon_Creek 9755103 2064 31.345 03.466 N39 W121 Kelley_Bar 9755109 2080 31.322 03.144 N39 W121 Below_Cherokee_Creek 9755107 2111 30.850 02.227 N39 W121 Below_Indian_Creek 9755113 2173 30.336 01.453 N39 W121 Hwy49_Bridge 9755105 2202 30.981 00.711 N39 W120 Indian_Valley 9755104 2268 31.132 59.915 N39 W120 Rocky_Rest 2000219 2306 30.782 58.570 N39 W120 Below_Convict_Flat 9755108 2353 31.225 57.371 N39 W120 Above_Convict_Flat 9755106 2453 31.542 56.203 N39 W120 Below_Goodyears_Bar 9755112 2669 32.475 54.307 N39 W120 Goodyears_Bar 2000236 2655 32.420 53.177 N39 W120 Above_Goodyears_Bar 9755111 2702 32.826 51.737 N39 W120 Below_Downieville 9755114 2889 33.551 49.933 N39 W120 Downie_River 9755110 3148 34.150 49.393 N39 W120 Downie_River 2000234 3148 34.150 49.393 N39 W120 Above_Downieville 1187552 3300 33.343 47.633 N39 W120 Below_Union_Flat 2232435 3353 33.706 44.871 N39 W120 Below_Haypress_Creek 2232415 4241 34.094 36.956 N39 W121 Canyon_Creek 2000218 2102 31.378 03.169

February 2012 Stillwater Sciences C-2

Appendix D

GEO Model Methods Tables

Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table D-1. Channel widths and depths measured at sites in the NY sub-basin (NMFS 2010, unpubl. data) Width (m) Depth (m) Drainage Site ID Length (m) area (km2) Bankfull Low Bankfull Low flow flow flow flow G2 584 9.2 6.38 nd 1.1 nd H10 206 18.3 11.87 5.1 0.8 0.3 G4 162 30.0 9.17 6.4 1.0 0.6 H5 131 42.7 16.70 9.6 1.3 0.4 H1 406 68.3 14.12 10.4 1.0 0.5 H2 285 81.0 11.62 8.3 1.0 0.4 G1 295 45.3 14.80 10.9 1.0 0.4 H4 831 119.3 19.29 14.6 1.1 0.5 H3 63 134.2 16.54 11.8 1.3 0.7 Log 14 195 186.6 15.18 9.7 1.6 0.9 Log 17 324 226.5 25.10 19.2 1.9 0.8 H6 285 239.4 24.10 18.7 1.5 0.8 H11 585 261.7 31.30 27.5 1.4 0.5 Log 16 689 310.6 28.96 13.5 1.6 0.8 H12 621 317.7 27.57 22.4 1.2 0.7 Log 12 455 569.1 29.38 17.8 1.5 1.0 H7 854 571.4 34.95 23.1 1.7 0.7 Log 11 542 572.8 34.90 25.4 1.6 0.7 H8 279 632.0 33.55 22.4 1.4 0.7 G3 Log7 610 664.1 39.04 nd 1.9 nd H9 483 702.1 46.36 38.1 1.5 0.8 G5 419 704.7 44.80 28.9 1.6 0.7 Log 2 801 738.0 45.44 33.4 1.6 0.9 Log Can 113 158.0 23.85 18.1 1.1 0.4 Log 1 662 900.0 41.86 34.0 2.3 1.0 “nd” indicates that data were not available.

Table D-2. Summary of model flow parameters at USGS gaging stations in upper Yuba River sub-basins. Drainage Model flow (cfs) Sub- Period of Gage Location 1 area 2 Winter Summer basin record 2 Bankfull (km ) base3 low4 11417500 SY Jones Bar near Grass Valley 1969–2011 798 4,289 553 47 11408850 MY Near Camptonville5 1969–1989 352 2,460 308 38 11413000 NY Below Goodyears Bar 1969–2011 648 4,572 739 126 1 Period of record used for this study. Period of record at gage may include additional water years. 2 1.5-year recurrence flow. 3 90% exceedance flow for the period January 1–April 30. 4 90% exceedance flow for the water year. Summer low flow for the NY gage below Goodyears Bar was not used in the modeling effort but is shown here for comparison. 5 USGS gage #11408850 (MY near Camptonville) characterizes flow in MY upstream of Our House Dam.

February 2012 Stillwater Sciences D-1 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table D-3. Modeled winter baseflow, bankfull flow, and summer low flow at USGS survey sites in the MY and SY sub-basins under current conditions. Drainage Estimated discharge1 (cfs) Sub- Location area basin Winter Bankfull Summer (km2) baseflow flow low flow Downstream of Milton Reservoir (#1) MY 110.3 97 770 12 Upstream of Gates of Antipodes (#1) MY 212.3 186 1,483 23 Gold Canyon at Seven Spot Mine MY 251.3 220 1,755 27 Upstream of Oregon Creek MY 417.9 366 2,918 45 Upstream of MY confluence MY 543.7 476 3,797 59 Laing's Crossing SY 313.8 218 1,687 18 Lower Golden Quartz Picnic Ground SY 383.1 266 2,060 23 Downstream of Humbug Creek SY 690.1 479 3,710 41 Edwards Crossing below Kenebek Creek SY 707.5 491 3,804 42 Upstream of Hwy 49 above Hoyt Crossing SY 794.8 551 4,274 47 Jones Bar Gage SY 819.0 568 4,404 48 Below Bridgeport SY 911.5 632 4,901 54 1 Predicted flow at USGS sites in SY were scaled from flow at USGS gage # 11417500 in SY. Predicted discharges at USGS sites in MY were scaled from flow at USGS gage # 11408850 in MY.

Table D-4. Best fit power law regressions relating reported widths (W) and depths (D) to modeled discharges (Q) at USGS survey sites in the MY and SY sub-basins under current conditions. Sub- Cross section location Depth Width basin Downstream of Milton Reservoir (#1) MY D = 0.1796 Q0.3534 W = 2.4038 Q 0.2707 Upstream of Gates of Antipodes (#1) MY D = 0.1108 Q 0.3937 W = 2.0265 Q 0.3614 Gold Canyon at Seven Spot Mine MY D = 0.1144 Q 0.4115 W = 3.9648 Q 0.2178 Upstream of Oregon Creek MY D = 0.2146 Q 0.2845 W = 4.9361 Q 0.3063 Upstream of MY confluence MY D = 0.0585 Q 0.4742 W = 5.1516 Q 0.2249 Laing's Crossing SY n/a1 W = 3.5668 Q 0.2382 Lower Golden Quartz Picnic Ground SY D = 0.0901 Q 0.3675 W = 7.2753 Q 0.2225 Downstream of Humbug Creek SY D = 0.1097 Q 0.3866 W = 4.2064 Q 0.2733 Edwards Crossing below Kenebek Creek SY D = 0.1122 Q 0.3768 W = 11.592 Q 0.1740 Upstream of Hwy 49 above Hoyt Crossing SY D = 0.2506 Q 0.3204 W = 8.5647 Q 0.1793 Jones Bar Gage SY D = 0.2464 Q 0.2967 W = 1.7358 Q 0.4097 Below Bridgeport SY D = 0.0777 Q 0.4224 W = 6.6535 Q 0.2117 1 No depth-discharge relationship was developed at Laing's Crossing due to uncertainties in the depth data.

February 2012 Stillwater Sciences D-2 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table D-5. Summer low flow width measured from aerial photography of sub-reaches between New Bullards Bar Dam and Rice’s Crossing. Mean Sub-reach n width Reach description (m) Upper 24 13.5 New Bullards Bar Dam to Middle Yuba River confluence Middle 58 15.0 Middle Yuba River confluence to New Colgate Powerhouse Lower 16 41.6 New Colgate Powerhouse to Rice's Crossing

February 2012 Stillwater Sciences D-3

e

Stillwater Sciences + 50 cfs + 100 cfs + 200 cfs ey sites under current conditions and for th under current conditions ey sites Current conditions

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

Watershed Yuba River in the Upper D-4 + 50 cfs + 100 cfs + 200 cfs rresponding channel width at 12 USGS surv rresponding channel width Estimated summer low discharge (cfs) (cfs) low discharge Estimated summer (m) low width Estimated summer Current conditions conditions SY 47 147 247 247 17.1 19.4 21.0 23.0 23.0 21.0 19.4 17.1 247 247 147 SY 47 Sub- basin additional flow releases specified under Alternative Management Scenarios 1 and 2. 1 and Scenarios Management Alternative under specified releases flow additional

Cross section location section Cross Estimated summer low flow discharge and co and discharge low flow summer Estimated Laing's Crossing Crossing Laing's Ground Picnic Quartz Golden Lower 12.9 Creek of Humbug Downstream 11.1 9.8 7.1 218 118 18 SY 68 Creek Kenebek below Crossing Edwards SY ofUpstream Hwy 49 above Hoyt SY Crossing 23 Gage Bar Jones SY 42 Bridgeport Below 73 (#1) Reservoir of Milton Downstream 41 142 (#1) Antipodes of Gates of Upstream 123 MY Mine Spot Seven at Canyon 141 Gold 242 Creek Oregon of Upstream MY 223 241 12 confluence of MY Upstream 242 MY 23 SY 14.6 SY 241 62 22.2 27 48 73 18.9 11.6 MY 54 112 25.4 MY 21.2 77 123 148 14.4 45 154 212 27.4 59 24.2 248 127 223 16.3 254 30.1 95 4.7 109 248 18.8 227 6.3 254 145 7.3 159 8.5 8.1 9.5 15.5 245 259 8.6 11.4 10.2 17.8 11.5 15.8 12.9 10.2 13.5 11.4 19.3 14.3 19.9 14.8 16.6 12.9 21.5 22.7 16.1 26.6 18.0 Table D-6. Technical Report Technical February 2012

Appendix E

North Yuba Sub-basin Channel Geometry and Habitat Type Data

(by area) area) (by % Run Run %

(by area) area) (by

% Riffle Riffle %

). area) (by

a

% Pool Pool % (by length) length) (by

Stillwater Sciences % Run Run % 22.6% 10.0% 67.5% 22.5% 22.6% 10.0% 67.5% 19.2% 19.0% 15.5% 65.3%

13.8% 29.1% 57.0% 13.9% 13.8% 29.1% 57.0% 4.3% 80.0% 4.6% 15.6% 22.2% 23.5% 26.3% 51.4% 11.8% 12.3% 31.6% 56.6% 43.0% 32.9% 33.4% 23.6% 39.4% 36.4% 14.0% 46.6% 26.9% 10.7% 61.7% 27.6% 26.9% 10.7% 61.7% 22.7% 17.9% 41.2% 36.1% 23.5% 24.3% 11.2% 65.3% 20.4% 22.3% 28.4% 51.2% (by length) length) (by

% Riffle Riffle %

(by length) length) (by

% Pool Pool %

depth (m) depth

f

Low Flow Flow Low

width (m) width

f slope. surveyed field the Low Flow Flow Low

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

depth (m) depth

e

Bankfull Watershed Yuba River in the Upper

1.00 8.34 0.43 11.6% 65.8% 11.6% 1.00 8.34 0.43 64.4% 16.6% 0.80 5.12 0.32

width (m) width

e

Bankfull Bankfull

(m) (m) reach length length reach units. habitat in individual n

E-1

Surveyed Surveyed 59.1% 216 27.1% 14.12 0.99 10.38 0.50 26.1% 614 41.0% 34.95 1.73 23.05 0.74 322 16.54 1.30 11.83 0.71 14.7% 80.7% 322 14.7% 16.54 1.30 11.83 0.71 55.4% 21.1% 0.42 9.60 1.27 235 16.70 54.4% 444 33.3% 24.10 1.45 18.70 0.77 41.3% 832 22.3% 46.36 1.47 38.08 0.82 387 19.29 1.13 14.60 0.51 14.2% 58.9% 387 14.2% 19.29 1.13 14.60 0.51 63.3% 586 12.4% 26.75 1.41 27.50 0.46 53.5% 570 24.2% 27.57 1.19 22.39 0.68 677 33.55 1.36 22.43 0.70 43.9% 38.2% 677 43.9% 33.55 1.36 22.43 0.70

slope

d comparable to not directly thus tat unit; Surveyed Surveyed

eloped by Stillwater Sciences, 2010). Sciences, 2010). Stillwater eloped by

class class

GIS slope slope GIS

GIS slope GIS

c

the average of measurements take of measurements average the

(km2)

b

Drainage area area Drainage flow (cfs) (cfs) flow

and not calculated directly the habi not calculated and over Mean daily daily Mean

sed on GIS coverage “yuba_geology” (dev “yuba_geology” coverage on GIS sed Date of survey survey of Date 10/13/11 144 261.7 1.1% 1–2% 1.5% 1–2% 261.7 10/13/11 144 1.1% 1.4% 1–2% 317.7 10/13/11 144 1.4% Channel and habitat type characteristics of each North Yuba sub-basin reachinsurveyed 2010 (NMFS, unpubl. data 10/5/2010 174 68.3 2.5% 2–4% 2.3% 10/7/2010 173 571.4 0.5% 0–1% 0.7% 10/5/2010 174 134.2 4.7% 4–8% 4.0% 10/6/2010 170 42.7 6.1% 4–8% 5.3% 10/6/2010 170 237.3 2.4% 2–4% 2.3% 10/8/2010 161 700.4 0.7% 0–1% 0.5% 10/6/2010 170 119.3 0.9% 0–1% 0.9% 10/7/2010 173 632.0 1.0% 1–2% 0.9%

Table E-1. name: Reach Cr. Cr. site) Pines NF Yuba Fiddle Cr. Fiddle Cr. Union Flat confluence confluence Salmon Cr. NF Yuba DS Downie River NF Yuba near NF Yuba near downstream of Goodyear's Bar Goodyear's Goodyear's Bar Goodyear's NF Yuba above

NF Yuba below NF Yuba below Loganville (MT Salmon Cr. near Salmon Cr. near below Lavezolla Upper Lavezolla Upper Lavezolla

NF Yuba @ Sierra NF Yuba @ Sierra Technical Report Technical February 2012 Reach ID ID Reach Field crew at all sites was J. Wooster and T. Holley, NMFS NMFS Holley, T. and Wooster J. was sites all at crew Field ba reach of end upstream at Estimated length. survey entire for the run over as rise Calculated “yuba_geology” GIS coverage from Identified reach. in taken were measurements multiple if of measurements Average not only, sites geometry hydraulic at of measurements Average H1 H2 Cr. 10/5/2010 174 Haypress 81.0 H3 3.5% 2–4% 2.3% 269 11.62 H4 H5 H6 H7 H8 3.4% 276 11.87 H9 4–8% 4.9% 18.3 146 Cr. 10/12/2010 H10 Cherokee H11 H12 a b c d e f Notes Notes

mm pool

high gravel high gravel

boulder scour boulder scour storage in pool storage in pool

tails, D50 22–32 D50 22–32 tails,

Bedrock type Bedrock

e

G, BB BB BB BB BB BB

L, G, L, G, RLL, RLL, RLL, RLL, RRL, RRL, RRL,

bedrock bedrock

exposed length with with length

Stillwater Sciences % of stream stream of %

Facies

d L = lateral control both sides L = lateral control both

l letter. G = gravel, C = Cobble, = C G = gravel, l letter.

D84 (mm) (mm) D84

D50 (mm) (mm) D50

D16 (mm) (mm) D16

depth (m) (m) depth Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run flow Low

rate is on the right with a capito a on the right with rate is ow bankfull, AB = above bankfull, AB = above ow bankfull,

Depth (m) (m) Depth

Bankfull Watershed Yuba River in the Upper

) m (

c flow width width flow

32 180 >256 gbC boulder steps

Geometry low low Geometry

e Upper Lavezolla Creek reach (NMFS, unpubl. data).

width (m) (m) width Bankfull Bankfull

E-2 13.96 9.45 0.94 0.40 32 180 >256 gbC

(m)

b flow width width flow

20 11.30 1.04 0.59 32 160 300 gbC Average low low Average

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

Local slope slope Local subst (dominant) e left and most pervasive

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation

% (secondary) (secondary) % Habitat unit data and channel geometry data for th geometry Habitat unit data and channel type Habitat ver left lateral control, G = exposed on ch exposed on = G lateral control, left ver

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

% (primary) (primary) % Habitat type type Habitat

Table E-2.

(secondary) (secondary)

Habitat type type Habitat Habitat type type Habitat run 100% 1.63 52.6 494.0 3.1% 9.40 14.27 32 160 300 gbC 100% pool 100% 1.15 pool 11.6 56.7 100% 9.9% 4.90 pool 0.46 24.8 255.4 100% 1.9% 10.30 0.03 15.5 131.1 32 0.2% 160 8.44 300 gbC 100% 32 160 300 gbC 100% 32 180 >256 gbC

riffle 100% riffle 0.06 20.7 235.6 100% 0.3% 11.40 riffle 0.04 13.2 100% 115.2 0.3% 8.75 0.32 10.2 98.7 32 3.1% 160 9.67 300 gbC 100% 32 160 300 gbC 32 30% 180 >256 gbC 50%

Technical Report Technical February 2012

unit ID ID unit Habitat Habitat B = boulder B = boulder of channel of channel habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e

A B C D E riffle F 100% 1 2 3 0.01 4 22.2 204.4 5 run Cumulative 0.0% riffle 9. riffle 100% 100% 100% 0.29 0.77 16.7 21.1 157.6 162.1 0.16 1.7% 4.92 3.6% 7.3 215.9 9.45 1,960.4 7.67 49.4 2.3% 2.2% 11.40 6.76 32 180 >256 gbC Notes Notes

Bedrock type Bedrock

e

BB BB

RLL, RLL, RLL,

bedrock bedrock

exposed exposed length with with length

Stillwater Sciences % of stream stream of %

lateral control both sides of channel channel sides of lateral control both

Facies

= boulder Cobble, B = C G = gravel, er. d

D84 (mm) (mm) D84 D50 (mm) (mm) D50 210 >256 gbC 210 >256 0% 200 >256 gbC 200 >256 0% gbC 200 >256 0% gcB 350 >256 0% >256 >256 gcB >256 0%

h (NMFS, unpubl. data). h (NMFS, D16 (mm) (mm) D16

64 64 64 64 64

    

depth (m) (m) depth Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run flow Low

rate is on the right with a capitol lett capitol a on the right with rate is ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull,

Depth (m) (m) Depth

Bankfull Watershed Yuba River in the Upper

) m (

c flow width width flow

the Haypress Creek reac the Haypress Creek Geometry low low Geometry

width (m) (m) width Bankfull Bankfull

E-3 11.21 8.32 1.12 0.45 220 gbC >256 0%

(m)

b

flow width width flow Average low low Average

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed Local slope slope Local subst (dominant) e left and most pervasive

1.2% 8.36 12.03 8.36 0.87 0.40 0.87 8.36 12.03 1.2% 8.36

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a Elevation Elevation

Habitat unit data and channel geometry data for geometry Habitat unit data and channel

% (secondary) (secondary) % Habitat type type Habitat ch exposed on = G lateral control, left ver

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t, % (primary) (primary) %

Table E-3. Habitat type type Habitat

(secondary) (secondary)

Habitat type type Habitat Habitat type type Habitat

Technical Report Technical February 2012

unit ID ID unit Habitat Habitat habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e 7 riffle 100% 0.94 30.40 307.0 3.1% 10.10 >256 >256 cB 0% 0% cB 0% cB >256 >256 >256 256 9.26 5.89 0.5% 7.78 1.2% 5.5% 12.60 356.7 8.32 128.5 10.10 4.8% 124.7 38.52 9.96 0.7% 3.1% 21.81 220.1 16.03 0.2 4.2% 326.0 187.1 307.0 0.27 0.88 17.47 524.3 39.00 22.49 100% 30.40 0.84 100% 0.48 52.64 100% 0.94 0.15 2.23 1 run 5.00 100% 30% 0.1% 2 riffle 100% 46.9 3 riffle 100% 100% 9.38 4 0.01 100% 100% 5 riffle pool 6 riffle 2.3% 7 riffle 2,417 8 run 9 riffle 269.49 10 6.09 Cumulative pool 100% 0.09 21.75 195.8 0.4% 9.00 >256 >256 cB 30% Notes Notes

low flow 1.1 m low flow 1.1

pool max depth at pool max depth

Bedrock type Bedrock

e

exposed bedrock bedrock exposed

length with with length % of stream stream of % Stillwater Sciences

lateral control both sides of channel channel sides of lateral control both

Facies

= boulder Cobble, B = C G = gravel, er. d

D84 (mm) (mm) D84

D50 (mm) (mm) D50 D16 (mm) (mm) D16

Salmon Creek reach (NMFS, unpubl. data). Salmon

(m) (m) Low flow depth depth flow Low

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

rate is on the right with a capitol lett capitol a on the right with rate is (m) (m) L = bankfull, AB = above ow bankfull, Bankfull Depth Depth Bankfull

Watershed Yuba River in the Upper

flow width (m) width flow

c

Geometry low low Geometry

(m) (m) Bankfull width width Bankfull 16.1 10.65 1.37 0.79 250 bC 0%

E-4

flow width (m) width flow

b

00 16.97 13 1.22 0.62 220 bC 0% Average low low Average Local slope slope Local

for the North Yuba River downstream of River downstream for the North Yuba annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

e left and most pervasive (dominant) subst (dominant) e left and most pervasive

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation

(secondary) (secondary) Habitat type % % type Habitat ch exposed on = G lateral control, left ver

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

(primary) (primary) Habitat type % % type Habitat

Habitat unit data and channel geometry data geometry Habitat unit data and channel (secondary) (secondary)

Habitat type type Habitat Habitat type type Habitat Table E-4.

Technical Report Technical February 2012 Habitat unit ID ID unit Habitat habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e 5 pool riffle 50% 50% 0.34 16.35 150.4 2.1% 9.20 256 bC 0% 0% bC 256 9.20 2.1% 150.4 16.35 0.34 50% 50% 8.28 13. 1 0% 1.8% 0.6% 2 1390.5 118.3 riffle 8.30 106.96 8.1% 14.29 100% 3 riffle 1.89 247.6 0.08 0% 29.83 cB 100% riffle 1,000 2.42 100% 4.04% 4 pool 7.99 5 pool 6.2% 3643 212.6 6 26.61 100% riffle 1.64 8.40 400 0% cB 7 322.47 8.7% 219.2 8 10.65 26.10 100% riffle 12.50 2.27 0.8% 13.04 500 0% cB 9 12.00 4.1% 158.4 run 537.3 14.87 0% cB 100% 10 12.5% 1,000 0.12 42.98 0% 100% cB riffle 1.75 1,000 15.00 233.8 Cumulative 19.48 0.4% 100% riffle 2.43 375.0 pool 100% 25.00 0.1 cB Notes Notes

scour at pool at pool boulders

some large pool from brx brx scour, pool pea gravel, with pea gravel, gravel riffle river gravel riffle pool created from from pool created bottom is sand and bottom is sand tail/velocity x-over x-over tail/velocity

Bedrock type Bedrock e AB AB AB RRL, RRL, RRL, RRL,

RLL, BB bedrock bedrock

Stillwater Sciences exposed exposed

length with with length

lateral control both sides of channel channel sides of lateral control both

% of stream stream of %

er. G = gravel, C = Cobble, B = boulder = boulder Cobble, B = C G = gravel, er.

Facies

d

reach (NMFS, unpubl. data). reach (NMFS, unpubl. (mm) D84

D50 (mm) (mm) D50

D16 (mm) (mm) D16 Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run (m) depth

rate is on the right with a capitol lett capitol a on the right with rate is Low flow flow Low L = bankfull, AB = above ow bankfull,

(m) Depth Watershed Yuba River in the Upper

Bankfull Bankfull

) m (

c

River below Lavezolla Creek River below Lavezolla flow width width flow

Geometry low low Geometry

width (m) (m) width

Bankfull Bankfull E-5

) m (

b

flow width width flow Average low low Average 15.80 21.5 17.4 0.89 0.38 16 100 0.38 15.80 21.5 0.89 17.4 gC 100% 11.80 17.07 11.8 1.37 0.65 45 180 500 gbC 100%

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

Local slope slope Local subst (dominant) e left and most pervasive

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation

% (secondary) (secondary) % Habitat type type Habitat ch exposed on = G lateral control, left ver

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

Habitat unit data and channel geometry data for the Downie geometry Habitat unit data and channel (primary) % type Habitat

(secondary) (secondary) Habitat type type Habitat

Table E-5. Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river 2 run riffle 50% 50% 0.17 32.92 559.6 0.5% 17.00 32 120 256 bgC 20% RRL, BB BB RRL, 20% bgC 256 120 BB BB 32 100% RRL, RRL, gbC 100% 100% gbS gbC >256 17.00 <4 100% 0.5% cG 559.6 75 0.6% 14.10 32.92 32 1,015.5 1.1% 9.10 0.17 8 64.27 870.3 8.30 1.1% 50% 61.72 0.38 0.1% 193.7 50% BB gbC 0% 0.68 168.3 21.29 bgC 0% 320 17.40 180 7.15 riffle RRL, 2.3% 0.9% 100% 100% 64 625.0 20.28 0.24 16.93 35.92 12.30 1 100% 1.4% 0.5% 463.0 0.34 2 run 727.8 0.1% 100% 3 42.99 riffle 0.02 195.8 0.6 15.92 166.2 100% 4 run 39.24 100% riffle 0.02 5 riffle 40% 23.24 0.9 60% 100% 6 riffle 7 riffle 0.11 pool 100% 8 pool 100% 9 riffle 0.92% 10 run 5,300 11 386.64 3.57 12 riffle 100% Cumulative 9.00 0.1 3.74 33.7 2.7% cG 32 60 pool 16 0% 100% 0.01 25.11 281.2 0.0% 11.20 100% RLL, BB a b c d e Notes Notes reach

gravel in pool-tail, gravel in in seen gravel first

Bedrock type Bedrock

e bedrock bedrock

exposed exposed

length with with length % of stream stream of % Stillwater Sciences

lateral control both sides of channel channel sides of lateral control both

Facies

d

er. G = gravel, C = Cobble, B = boulder = boulder Cobble, B = C G = gravel, er.

D84 (mm) (mm) D84

D50 (mm) (mm) D50

D16 (mm) (mm) D16

depth (m) (m) depth Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run flow Low

rate is on the right with a capitol lett capitol a on the right with rate is ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull,

Depth (m) (m) Depth

Bankfull Watershed Yuba River in the Upper

) m (

c

flow width width flow Geometry low low Geometry

mon Creek near confluence reach (NMFS, unpubl. data). mon Creek near confluence reach (NMFS, width (m) (m) width

90 300 > 1000 gcB 0% step-pool Bankfull Bankfull

15.4 6.6 1.37 0.37 100 240 >1,000 bC >1,000 240 100 0% 0.37 15.4 6.6 1.37 E-6

(m)

b flow width width flow

00 0% >256 cB step-pool Average low low Average 0.47 1.17 12.6 9.00 18 cB 0%

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

Local slope slope Local subst (dominant) e left and most pervasive

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation

% (secondary) (secondary) % Habitat type type Habitat ch exposed on = G lateral control, left ver

Habitat unit data and channel geometry data for Sal geometry Habitat unit data and channel

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

% (primary) (primary) % Habitat type type Habitat

Table E-6. (secondary)

Habitat type type Habitat Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e 4 run riffle 80% 20% 0.58 29.74 133.8 2.0% 4.50 130 300 600 cB 0% 0% cB 600 0% 300 cB 130 0% >256 0% cB 0% cB cB 0% 6. >500 bC 4.50 6.60 3.9% 0% 2.0% 8.10 240 4.2% 2.4% cB 125.0 5.10 12.3% 133.8 159.7 4.00 6.5% 272.7 20.83 110.7 29.74 24.19 10.1% 147.3 0.81 6.50 30.30 13.67 0.58 1.01 47.6 10.90 5.74 28.88 10% 14.2% 0.74 1.68 6.60 20% 3.5% 11.91 0.6% 90% 1.88 60.4 100% 25% 10.0% 80% 342.7 1.2 49.9 100% riffle 9.29 75% 135.3 100% 31.44 riffle 8.70 1 riffle 1.32 2 pool 100% 20.50 riffle 3 riffle 1.11 0.05 4 run 5 riffle 2.06 20% 100% 6 run 7 riffle 100% 80% 100% 8 9 riffle riffle pool 10 run 100% 11 riffle 0.3% 0.02 12 pool 7.20 5.80 41.8 Cumulative 5.3% 1,627 235.25 32 160 12.46 300 gcB 0% Notes Notes

mm pool pool depth

pool-tail is dominated by by dominated bedrock scour bedrock scour bedrock scour bedrock scour bedrock scour gravel 45 to 64 to 64 gravel 45 pool, pool-tail is is pool, pool-tail cobble with D50 cobble with = 110, > 3 m max

Bedrock type Bedrock

e

BB BB BB AB

RLL, RLL, RLL, RLL, RLL, RRL, RRL, RRL, BB, G

bedrock bedrock exposed exposed

Stillwater Sciences length with with length % of stream stream of % channel sides of lateral control both

er. G = gravel, C = Cobble, B = boulder = boulder Cobble, B = C G = gravel, er.

Facies

d D84 (mm) (mm) D84

s reach (NMFS, unpubl. data). s reach (NMFS, unpubl.

D50 (mm) (mm) D50

D16 (mm) (mm) D16 depth (m) (m) depth

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

Low flow flow Low lett capitol a on the right with rate is ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull, Depth (m) (m) Depth

Watershed Yuba River in the Upper Bankfull Bankfull

(m)

ba River at the Sierra Pine ba c

flow width width flow

Geometry low low Geometry

width (m) (m) width

Bankfull Bankfull E-7

(m)

b

flow width width flow Average low low Average

18.70 24.1 18.7 18.70 0.77 1.45 0%

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

Local slope slope Local subst (dominant) e left and most pervasive

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation

% (secondary) (secondary) % Habitat type type Habitat ch exposed on = G lateral control, left ver

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

% (primary) (primary) %

Habitat unit data and channel geometry data for the North Yu geometry Habitat unit data and channel Habitat type type Habitat

(secondary) (secondary) Habitat type type Habitat

Table E-7. Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e 7 riffle 100% 2.14 41.57 644.3 5.1% 15.50 >256 cB 0% 0% cB 0% cB 2.9% >256 1,065.9 >300 57.00 1.63 30% 15.50 70% 17.50 5.1% run 0% 20.00 0.3% cB 0% 644.3 473.8 3.6% 0 riffle 23.69 16.30 1 0.08 2 24.50 0.3% 41.57 945.9 15.60 2.5% 100% 395.1 3 688.5 28.10 riffle 100% 4.3% 0.7 24.24 gC 4.83 75.3 pool 80 gbC 0% 0.21 220 0% 100% 0.07 54.05 riffle 2.14 4 75% 100% gcB pool 18.20 1.96 5 0.2% 13.60 645.4 4.4% 776.2 100% 57.07 35.46 2.53 riffle 100% cB 400 100% 0.08 6 100% 100% pool 7 riffle 8 10.90 14.30 9 riffle 0.3% 297.6 27.30 0.9% 2.3% 769.1 pool 53.78 0.08 100% 10 gbC 0.5 7,259 75% 240 30% bC 220 444.43 70% 75% riffle 11 run 10.05 Cumulative pool 100% 0.07 37.34 481.7 0.2% 12.90 50% Notes Notes margin

bedrock constriction constriction main pool is main pool pool scour at pool scour but tail out is sand and fine sand and bedrock scour bedrock scour bedrock scour gravel at main main at gravel cobble dominated boulder dominated boulder on channel channel boulder on on run margin with on run margin

narrow pool habitat narrow pool habitat bedrock scour pool, pool, bedrock scour

Bedrock type Bedrock

e

bedrock bedrock Stillwater Sciences exposed exposed

lateral control both sides of channel channel sides of lateral control both length with with length

er. G = gravel, C = Cobble, B = boulder = boulder Cobble, B = C G = gravel, er. % of stream stream of %

Facies

d

reach (NMFS, unpubl. data). reach (NMFS,

D84 (mm) (mm) D84

D50 (mm) (mm) D50

D16 (mm) (mm) D16 Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run (m) depth

rate is on the right with a capitol lett capitol a on the right with rate is

ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull,

Low flow flow Low

(m) Depth Watershed Yuba River in the Upper

Bankfull Bankfull

(m) a River above Goodyear's Bar Bar Goodyear's a River above

c

flow width width flow

Geometry low low Geometry width (m) (m) width

3 23.5 1.73 0.74 64 130 256 gbC 100% RLL, BB gbC 256 100% 64 130 0.74 RLL, 3 23.5 1.73

E-8 Bankfull Bankfull

(m)

b

20 34.6 22.6 240 bC 100% RRL, BB RRL, 100% width bC 240 flow 22.6 34.6 20 Average low low Average 15.90 100 220 500 bC 75% RRL, BB RRL, 75% bC 500 220 100 15.90

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

e left and most pervasive (dominant) subst (dominant) e left and most pervasive 33.70 32 100 180 gC 0% gC 180 100 32 33.70

Local slope slope Local

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation % (secondary) (secondary) %

ver left lateral control, G = exposed on ch exposed on = G lateral control, left ver Habitat type type Habitat

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t, % (primary) (primary) %

Habitat unit data and channel geometry data for the North Yub geometry Habitat unit data and channel type Habitat

(secondary) (secondary) Habitat type type Habitat

Table E-8. Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e 2 pool 100% 0.22 114.23 1,964.8 0.2% 17. 0.2% 1,964.8 114.23 BB 0.22 RRL, 100% cB 35. 350 BB 100% 23.50 13.20 RLL, 20% 0.2% gC 0.3% 1 642.6 27.40 2 pool 160 0.8% 610.7 48.68 cG 22.29 3 90 0% 80 752.7 BB 45 1.7% riffle 100% 0.18 16 0.1 1,087.2 22 68.38 4 100% riffle 100% 1.16 10.30 RRL, 60% 32.03 0.3% 37.40 pool 364.9 35.43 0.4% 5 8.45 0.1 0.1 1.3% 3,643.9 244.5 28.94 BB 30% 6 riffle 100% 0.38 70% 97.43 bC 200 80% RRL, pool 0.4 7 run 3.2% 8 1,374.6 100% 100% 40.79 riffle 100% 1.32 9 run BB 10 0.2% 29.60 1,868.4 63.12 25.10 11 run 0.13 RLL, 100% 0.1% bgC run 75% 25% pool 962.8 38.36 256 pool 100% 0.02 100 0.7% 32 12 BB 14,070 bgC 256 100% 613.7 100 RLL, 32 Cumulative 4.15 pool 100% 0.04 24.02 552.5 0.2% 23.00 22 140 bgC 100% RLL, BB Notes Notes

in-channel in-channel and bedrock and bedrock sand and gravel sand and gravel - both lateral and - both lateral and covering boulders boulders covering bedrock scour pool pool bedrock scour

Bedrock type Bedrock e AB

RRL, RRL, RRL, RRL, RRL,

BB, G BB, G BB, G BB, G

bedrock bedrock Stillwater Sciences exposed exposed

lateral control both sides of channel channel sides of lateral control both length with with length % of stream stream of %

letter. G = gravel, C = Cobble, B = Cobble, B = C G = gravel, letter.

Facies

d

cB 100% RRL, BB pool bedrock scour r reach (NMFS, unpubl. data). r reach (NMFS, (mm) D84 cB 100% 100%

00 >10 D50 (mm) (mm) D50

> >

300 500

D16 (mm) (mm) D16 Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run (m) depth

rate is on the right with a capitol capitol a on the right with rate is

ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull,

350 cB 100% RRL, BB pool bedrock scour Low flow flow Low

(m) Depth Watershed Yuba River in the Upper

Bankfull Bankfull

(m)

ba River below Goodyear's Ba Goodyear's River below ba c

flow width width flow

Geometry low low Geometry AB bgC 256 64 150 0.64 50% 25.3 1.37 RLL, width (m) (m) width

E-9

Bankfull Bankfull 9

35.4

(m)

b

flow width width flow Average low low Average 19.55 31.6 19.55 1.35 0.76 64 19.55 31.6 19.55 1.35 gbC 180 300 100% BB RRL, 100% bgC 180 23.00

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

e left and most pervasive (dominant) subst (dominant) e left and most pervasive 26.10 100 256 400 cB 0% AB cB 400 256 100 26.10 Local slope slope Local

0.2% 30.30 32 120 256 bgC 100% bgC 256 120 32 30.30 0.2%

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation % (secondary) (secondary) %

ver left lateral control, G = exposed on ch exposed on = G lateral control, left ver Habitat type type Habitat

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t, % (primary) (primary) %

Habitat unit data and channel geometry data for the North Yu geometry Habitat unit data and channel type Habitat

(secondary) (secondary) Habitat type type Habitat

Table E-9. Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat boulder habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e 4 run 100% 0.3 49.82 1,226.1 0.6% 24.61 220 gbC 0% 1,288.1 AB gbC 220 42.51 24.61 0.08 0.6% 0.1% 1,226.1 1 2.0% 49.82 1,438.4 25% 2 1,075.4 55.01 0.3 3 riffle 100% 16.30 1.1 2.9% 0.1% 703.0 4 1,324.6 43.13 100% pool 62.54 50.75 100% 0.04 75% 5 riffle 100% 1.47 run 15.28 0.2% 1,025.7 6 300 0.09 67.13 10.70 pool 100% riffle 140 0.11 1.2% 407.6 38.09 7 riffle 100% 0.46 11.50 3.9% 319.8 27.81 8 pool riffle 100% 1.08 100% 9 22.60 bgC 50% 1.3% 617.2 10 240 27.31 28.80 120 11 pool 0.6% riffle 100% 0.35 gC 22 1,110.0 0% 220 25.30 38.54 12 run 140 0.9% 100% 0.22 32 1,229.6 48.60 13 0.89% riffle 100% 0.46 30.10 14,663 0.5% BB 987.3 14 32.80 run 676.75 100% 0.18 RLL, 100% gbC Cumulative 220 6.03 pool 100% 0.09 92.71 1909.8 0.1% 20.60 100% RLL, BB Notes Notes left

upstream riffle HU #5 and at bedrock and at bedrock pool created as pool created large gravel and gravel large and coarser than than and coarser pea gravel on top top on pea gravel channel reconnect channel reconnect outcrop, veneer of outcrop, veneer cobble bar on river on river cobble bar Kokanee spawning Kokanee spawning this riffle is steeper is steeper this riffle mid-channel island,

Bedrock type Bedrock e RLL, RLL,

BB, G

bedrock bedrock Stillwater Sciences exposed exposed

lateral control both sides of channel channel sides of lateral control both length with with length

er. G = gravel, C = Cobble, B = boulder, = boulder, Cobble, B = C G = gravel, er. % of stream stream of %

Facies

d

reach (NMFS, unpubl. data). reach (NMFS, (mm) D84

D50 (mm) (mm) D50

D16 (mm) (mm) D16 Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run (m) depth

rate is on the right with a capitol lett capitol a on the right with rate is

ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull,

Low flow flow Low

(m) Depth Watershed Yuba River in the Upper

Bankfull Bankfull

(m)

c flow width width flow

h Yuba River below Fiddle Creek h Yuba River below

Geometry low low Geometry 0.78 36.8 1.64 180 gbC 0%

width (m) (m) width Bankfull Bankfull E-10

2

45.8

(m)

b

flow width width flow 50 46.9 39.35 1.3 0.85 75 gbC 200 350 0% Average low low Average 22.70 8 75 220 bgC 25% RRL, BB RRL, 25% bgC 220 75 8 22.70

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

e left and most pervasive (dominant) subst (dominant) e left and most pervasive Local slope slope Local

2% 50.30 64 150 256 gbC 0% gbC 256 0% gbC 150 400 64 200 50.30 75 2% 51.45 6%

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation % (secondary) (secondary) %

ver left lateral control, G = exposed on ch exposed on = G lateral control, left ver Habitat type type Habitat

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

Habitat unit data and channel geometry data for the Nort channel geometry data and Habitat unit (primary) % type Habitat

(secondary) (secondary) Habitat type type Habitat

Table E-10. Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat BR = bedrock BR = bedrock habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e 5 riffle run 60% 40% 0.23 117.43 5,906.7 0. 5,906.7 117.43 0.1% 0.23 2,062.1 40% 90.84 60% 1 27.95 1.2% 648.7 2 23.21 run 0.06 26.62 riffle 100% 0.27 0.1% bgC 40% gbC 3 33. 0% 150 2,514.9 240 0.4% 94.49 4 2,303.5 120 pool 100% 0.11 32 68.76 47.40 5 riffle 0.1% riffle 100% 0.28 6001.3 gC 0% 126.61 180 run 90 spawning 100% 11 0.14 100% 6 1. 7,158.8 Kokanee 139.14 riffle 100% 2.28 7 pool 8 31.50 0.1% bgC 0.5% 0% 1,975.7 300 9 36.80 32,632 62.72 run 0.8% 100 100% 0.08 22 1,555.2 831.57 10 42.26 Cumulative riffle 100% 0.33 3.98 run 100% 0.2 66.11 2,505.6 0.3% 37.90 64 140 300 bgC 0% Notes Notes

reach of alluvium be a step-pool be a step-pool step-pool reach step-pool reach channel margins, margins, channel velocity shadows velocity shadows slow water doesn't doesn't slow water

some fine gravel on some fine gravel down to bedrock on down to bedrock lateral bedrock scour scour lateral bedrock

some gravel stored in in stored gravel some channel bed = no pool = no channel bed bedrock creating steps bedrock creating depth with thin mantle mantle thin depth with in this step-pool reach, reach, step-pool in this have depth for pools to for pools have depth almost a "step-run" but almost a "step-run"

Bedrock type Bedrock e BB BB BB BB BB G, L, G, L, G, L, G, L, RRL, RRL, RRL, G, BB G, BB

Stillwater Sciences bedrock bedrock

exposed exposed

length with with length

% of stream stream of %

Facies

d D84 (mm) (mm) D84

100% D50 (mm) (mm) D50

B

BR, D16 (mm) (mm) D16

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

depth (m) (m) depth Low flow flow Low

Watershed Yuba River in the Upper Depth (m) (m) Depth

Bankfull Bankfull

) m (

c

r the Cherokee Creek reach (NMFS, unpubl. data). r the Cherokee Creek reach (NMFS, width flow

Geometry low low Geometry width (m) (m) width

E-11 Bankfull Bankfull

12.24 4.42 0.71 0.28 45 0.71 12.24 4.42 bgC 130 250 BB 20% G,

(m)

b

flow width width flow Average low low Average

25.31 11.5 5.82 0.89 0.36 0.89 25.31 11.5 5.82 200 bC 25%

Local slope slope Local

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a Elevation Elevation

Habitat unit data and channel geometry data fo channel geometry data and Habitat unit

% (secondary) (secondary) %

Habitat type type Habitat

% (primary) (primary) % Table E-11. type Habitat

(secondary) (secondary)

Habitat type type Habitat Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat 3 run 100% 0.15 27.47 754.6 0.5% 27.47 220 gbC 0% gbC 220 27.47 1 0.5% 2 25.63 754.6 4.6% 75% 656.9 27.47 25.63 3 gbC riffle pool 24.38 riffle 100% 1.19 60% 0.15 0.35 16.93 40% 286.6 2.1% 3.4% 16.93 100% run 4 594.4 20.07 5.8% 24.38 100% 402.8 BR 20.07 5 24.82 0.84 100% riffle 100% 1.17 cB 300 1.3% 100% riffle 616.0 24.82 gbC 100 180 300 6 0% 0.32 100% run 7 27.23 4.7% 741.5 27.23 riffle 100% 1.27 cB 75% 256 8 25.17 25.17 633.5 1.4% 9 0.35 24.06 gbC 80% 20% 0% riffle pool 5.9% 400 578.9 10 24.06 220 64 riffle 100% 1.42 25.31 640.6 1.8% 11 0.45 75% 25% riffle pool 22 BR 100% riffle 100% 1.78 34.85 1,214.5 5.1% 34.85 Notes Notes

Bedrock type Bedrock e

Stillwater Sciences bedrock bedrock

exposed exposed channel sides of lateral control both

length with with length = boulder, Cobble, B = C G = gravel, er.

% of stream stream of %

Facies

d

D84 (mm) (mm) D84

D50 (mm) (mm) D50 D16 (mm) (mm) D16

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

depth (m) (m) depth lett capitol a on the right with rate is ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull, Low flow flow Low

Watershed Yuba River in the Upper Depth (m) (m) Depth

Bankfull Bankfull

) m (

c

flow width width flow

Geometry low low Geometry width (m) (m) width

E-12 Bankfull Bankfull

(m)

b

flow width width flow Average low low Average

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

e left and most pervasive (dominant) subst (dominant) e left and most pervasive

Local slope slope Local

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation % (secondary) (secondary) %

ver left lateral control, G = exposed on ch exposed on = G lateral control, left ver Habitat type type Habitat

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

% (primary) (primary) % type Habitat

(secondary) (secondary)

Habitat type type Habitat Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat BR = bedrock BR = bedrock habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e Cumulative 9.29 275.92 7,120 3.4% 3.4% 7,120 275.92 Cumulative 9.29 Notes Notes

step

in bars

coarse gravel gravel coarse large boulder high volumes of high volumes of sediment storage sediment storage sediment storage sediment storage moving into high moving into high pool scour around around pool scour small pool / pocket / pocket small pool scour around LWD scour around

grain size decreases, abundant medium to abundant medium

bedrock creating steep steep bedrock creating reach—in-channel and reach—in-channel wide valleywidth with

Bedrock type Bedrock e BB BB ent in- ent in-

outcrop outcrop RLL,G, RLL,G, RLL,G, channel channel channel intermitt intermitt

Stillwater Sciences

bedrock bedrock

exposed exposed length with with length

(NMFS, unpubl. data).

% of stream stream of %

Facies

d

D84 (mm) (mm) D84

B 100% B D50 (mm) (mm) D50

lle (MT site) reach

B, BR D16 (mm) (mm) D16

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

depth (m) (m) depth Low flow flow Low

Watershed Yuba River in the Upper

Depth (m) (m) Depth

Bankfull Bankfull

(m)

c

flow width width flow

Geometry low low Geometry

width (m) (m) width E-13

Bankfull Bankfull

) m (

b

flow width width flow BB 32 0.46 gC 90 160 31.3 27.5 1.41 10% 00 RLL, for the North Yuba River near Loganvi for the North Yuba River near

Average low low Average

14.28 80 150 300 gbC 20% RLL, BB RLL, 20% gbC 300 150 80 14.28

Local slope slope Local

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation

% (secondary) (secondary) %

Habitat type type Habitat

% (primary) (primary) % type Habitat Habitat unit data and channel geometry data channel geometry data and Habitat unit

(secondary) (secondary)

Habitat type type Habitat Table E-12. type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat 1 pool 100% 0.05 25.08 428.9 0.2% 17.10 22.2 200 gbC 100% RLL, BB RLL, 100% gbC 200 22.2 13.70 17.10 0% BB 0.1% bgC 0.2% 364.8 428.9 256 25.08 26.63 G, 10% 1 100% 0.05 120 cB bgC 0.03 BB 2 16.10 11.00 100% 2.1% 64 pool 764.1 3 6.8% 220 100% RLL, 47.46 100% cB 84.4 256 riffle 100% 1.02 7.67 110 pool 4 13.50 0.52 100% 45 5 0.3% riffle 9.80 BB 0.4% 418.1 116.4 11.20 11.88 6 18.80 pool RLL, 100% 30.97 0.05 100% 3.8% gbC 160 0.6% 698.8 37.17 gbC 0% 0.08 180 7 riffle 100% 1.41 444.2 8 100% 39.66 9 run 0.23 1.6% riffle 1,027.5 71.98 100% 10 100% riffle 100% 1.18 1.86 69.28 run 969.9 11 14.00 2.7% 12 riffle run 65% 35% 0.45 55.84 18. 1,005.1 0.8% 25.00 26.63 bgC 5% 665.8 0.5% 23.85 0.12 13 run 85% 15% pool 220 100 180 350 bC 1.5% 970.2 120 40.68 0% 45 riffle 100% 0.59 bgC 300 0% 140 64 14 18.56 34.80 645.9 0.6% 0.21 run 85% 15% pool 110 bgC 5% Notes Notes

Bedrock type Bedrock e ent in-

outcrop channel channel intermitt

Stillwater Sciences bedrock bedrock

lateral control both sides of channel channel sides of lateral control both exposed exposed

er. G = gravel, C = Cobble, B = boulder, = boulder, Cobble, B = C G = gravel, er. length with with length

% of stream stream of %

Facies

d

D84 (mm) (mm) D84

D50 (mm) (mm) D50 D16 (mm) (mm) D16

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

rate is on the right with a capitol lett capitol a on the right with rate is

ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull, depth (m) (m) depth Low flow flow Low

Watershed Yuba River in the Upper

Depth (m) (m) Depth

Bankfull Bankfull

(m)

c

flow width width flow

Geometry low low Geometry

width (m) (m) width E-14

Bankfull Bankfull

) m (

b

flow width width flow Average low low Average

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

e left and most pervasive (dominant) subst (dominant) e left and most pervasive

Local slope slope Local

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation % (secondary) (secondary) %

ver left lateral control, G = exposed on ch exposed on = G lateral control, left ver Habitat type type Habitat

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

% (primary) (primary) % type Habitat

(secondary) (secondary)

Habitat type type Habitat Habitat type type Habitat

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat BR = bedrock BR = bedrock habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e Cumulative 8.61 585.99 9,906 1.5% 1.5% 15 9,906 585.99 Cumulative 8.61 riffle 100% 0.81 60.26 1,301.6 1.3% 21.60 45 140 275 bgC 5% Notes Notes

5)

LWD scour large alluvial bar bar alluvial large (macro point-bar) (macro point-bar) bedrock scour pool pool bedrock scour pool created around around pool created stream channel flows flows channel stream

around large boulder, around large boulder, gravel, and cobble bar gravel, and cobble

bedrock wall (H.U.s 2– bedrock wall alluvial reaches with LB with LB reaches alluvial channel cuts back across across back cuts channel

Bedrock type Bedrock e BB BB BB BB AB RLL, RLL, RLL, RLL, RLL, RLL, RLL,

Stillwater Sciences bedrock bedrock

exposed exposed channel sides of lateral control both

length with with length = boulder Cobble, B = C G = gravel, er.

% of stream stream of %

Facies

d

D84 (mm) (mm) D84

Union Flat reach (NMFS, unpubl. data). Union Flat reach (NMFS, (mm) D50 D16 (mm) (mm) D16

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run

depth (m) (m) depth lett capitol a on the right with rate is ow bankfull, AB = above bankfull, L = bankfull, AB = above ow bankfull, Low flow flow Low

Watershed Yuba River in the Upper Depth (m) (m) Depth

Bankfull Bankfull

(m)

c

flow width width flow

Geometry low low Geometry

width (m) (m) width

E-15

Bankfull Bankfull

) m (

b

flow width width flow 50 27.57 22.39 1.19 0.68 75 160 275 gbC 0%

for the North Yuba River downstream of for the North Yuba River downstream Average low low Average

annel bed and/or grade control, BB = bel BB grade control, and/or annel bed

e left and most pervasive (dominant) subst (dominant) e left and most pervasive Local slope slope Local

3% 19.20 75 150 250 gbC 100%

Area (m2) (m2) Area

Length (m) (m) Length

difference (m) difference

a

Elevation Elevation % (secondary) (secondary) %

ver left lateral control, G = exposed on ch exposed on = G lateral control, left ver Habitat type type Habitat

ith the lowest % on the channel bed is on th bed channel the % on lowest the ith t, not measurement at location of hydraulic geometry measurement locations. locations. measurement geometry hydraulic of location at measurement not t,

% (primary) (primary) % type Habitat Habitat unit data and channel geometry data channel geometry data and Habitat unit

(secondary) (secondary)

Habitat type type Habitat Habitat type type Habitat Table E-13.

Technical Report Technical February 2012

ID ID Habitat unit unit Habitat habitat uni width for Average low flow w substrate that such written are Facies (length). run over difference) (elevation rise as Calculated taken. were measurements geometry hydraulic where sections cross section cross at specific Low flow width = ri RLL control, lateral right RRL = river a b c d e 1 10.90 2.8% 509.8 46.77 bC riffle 100% 1.32 15% 220 2 13.90 0.6% 423.4 3 18.67 30.46 run 100% 0.0% 0.19 bC 240 50% 1,220.6 4 65.38 100% 1. pool gbC 100% 0.03 240 1,224.4 5 18.13 63.77 riffle 100% 0.8 13.50 0.1% 6 1,084.5 3.6% 59.82 100% 7 1,146.8 pool bgC 100% 0.06 140 84.95 cB 8 11.24 10.80 275 0% riffle 100% 3.02 0.4% 2.3% 248.7 263.3 9 22.13 24.38 run 16. 100% 0.09 bC riffle 100% 0.57 180 gbC 0% 0% 1.7% 10 1.4% 160 1,403.7 8,881 17.00 11 42.19 85.07 717.2 0.4% 0.17 run 70% 30% pool 569.86 Cumulative riffle 100% 1.48 8 run 160 gbC 0% 100% 0.27 44.94 638.1 0.6% 14.20 64 130 220 bgC 0%

Appendix F

Spring-run Chinook Salmon HAB Module Methods and Tables

Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

HABITAT TYPES

Table F-1. Fraction of pool, riffle, run, and cascade habitat types by channel length for each channel gradient category used to parameterize the spring-run Chinook salmon and steelhead HAB modules for the SY, MY, NY, and NBB model sub-basins. The same values were used for each model scenario. Data sources: SY and MY – Stillwater Sciences (2006b); NY – NMFS (2010 unpubl. data), see Appendix E of this report; NBB – HDR|DTA 2010 unpubl. data). Channel Model reach Pool Riffle Run Cascade gradient class SY 0.490 0.205 0.304 0.001 MY 0.466 0.231 0.303 0.000 0–1% NY 0.269 0.400 0.332 0.000 NBB 0.496 0.163 0.341 0.000 SY 0.455 0.301 0.241 0.003 MY 0.455 0.293 0.251 0.000 1–2% NY 0.277 0.510 0.213 0.000 NBB 0.496 0.163 0.341 0.000 SY 0.458 0.390 0.147 0.005 MY 0.428 0.289 0.281 0.002 2–4% NY 0.256 0.588 0.157 0.000 NBB 0.496 0.163 0.341 0.000 SY 0.433 0.400 0.125 0.042 MY 0.440 0.384 0.169 0.007 4–8% NY 0.172 0.682 0.147 0.000 NBB 0.496 0.163 0.341 0.000 SY 0.311 0.603 0.000 0.087 MY 0.199 0.512 0.289 0.000 8–12% NYa 0.274 0.573 0.095 0.058 NBB 0.496 0.163 0.341 0.000 a NMFS did not collect data at sites with gradients >8% in the NY; therefore combined MY and SY data were used.

February 2012 Stillwater Sciences F-1 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

HOLDING

Table F-2. Usable fraction data and calculations for spring-run Chinook salmon holding habitat in the MY and SY sub-basins under each alternative management scenario. The values in the last column were used to parameterize the RIPPLE HAB module for the SY and MY sub-basins. The same usable fraction values were applied to each gradient class since the data reflect the actual number of holding pools documented in each SY and MY reach. River Fraction Fraction miles of each Usable Number Number of pools Sub- thermally holding fraction Scenarioa of holding of total that are basin suitable pool of pools in poolsc poolsd holding for usable for reach pools holdingb holding SY S1 7.0 7 57 0.12 0.75 0.09 SY S2 15.3 12 117 0.10 0.75 0.08 MY CC 2.3 12 32 0.38 0.50 0.19 MY S1 11.9 17 117 0.15 0.75 0.11 MY S2 22.5 21 209 0.10 0.75 0.08 a No habitat would be thermally suitable for holding in the SY under current conditions. b Mainstem channels only. c Source: Vogel (2006). d Source: Stillwater Sciences (2006b).

Table F-3. Usable fraction of and calculations for spring-run Chinook salmon holding habitat for each channel gradient category in the SY and MY sub-basins. The values in the last column were used to parameterize the RIPPLE HAB module for the NY and NBB sub-basins. No data on the number of holding pools were available for the NY or NBB sub-basins; therefore data from the SY and MY were stratified by gradient category and used to derive usable holding fraction parameters for the NY and NBB sub-basins.

Fraction of Number of Number of Fraction of Gradient each holding Usable fraction holding pools total pools in pools that are category pool usable for of pools in SY and MY SY and MY holding pools holding

0–1% 16 158 0.10 0.50 0.051 1–2% 25 348 0.07 0.50 0.036 2–4% 40 235 0.17 0.50 0.085 4–8% 14 83 0.17 0.50 0.084 8+% 5 16 0.31 0.50 0.156

February 2012 Stillwater Sciences F-2 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

SPAWNING

Table F-4. Values used to parameterize the RIPPLE HAB module for spring-run Chinook salmon spawning density and fraction of the channel usable for spawning for each habitat type and channel gradient combination in the SY, MY, and NY model runs. The same values were used for each model scenario. It was assumed that spawning does not occur in cascade habitats. Pool Riffle Run Channel Density Density Density Model Usable Model Usable Model Usable gradient (females (females (females run fraction run fraction run fraction /m2) /m2) /m2) SY 0.0282 SY 0.0084 SY 0.0057 0–1% MY 0.0381 0.185a MY 0.0096 0.185a MY 0.0073 0.185a NY 0.0321 NY 0.0088 NY 0.0063 SY 0.0248 SY 0.0047 SY 0.0059 a a a 1–2% MY 0.0421 0.185 MY 0.0082 0.185 MY 0.0095 0.185 NY 0.0326 NY 0.0062 NY 0.0075 SY 0.0093 SY 0.0014 SY 0.0036 a a a 2–4% MY 0.0186 0.185 MY 0.0034 0.185 MY 0.0035 0.185 NY 0.0134 NY 0.0022 NY 0.0034 SY 0.0055 SY 0 SY 0 4–8% MY 0.0183 0.185a MY 0 0b MY 0 0b NY 0.0117 NY 0 NY 0 a Assumes one female per redd with an average size of 5.4 m2. b Assumes spawning does not occur in riffles or runs with channel gradients ≥ 4%.

Table F-5. Values used to parameterize the RIPPLE HAB module for spring-run Chinook female spawning density and usable fraction of spawning for each habitat type and channel gradient combination in the NBB model runs for Current Conditions (CC), Scenario 1 (S1), and Scenario 2 (S2). It was assumed that spawning does not occur in cascade habitats. Pool Riffle Run Channel Density Density Density Usable Usable Usable gradient Scenario (females Scenario (females Scenario (females fraction fraction fraction /m2) /m2) /m2) CC 0.0082b CC 0.0031b CC 0.0015b 0–1% S1 0.0160 0.18a S1 0.0044 0.18a S1 0.0032 0.18a S2 0.0321 S2 0.0088 S2 0.0063 CC 0.0021b CC 0.0008b CC 0.0004b 1–2% S1 0.0163 0.18a S1 0.0031 0.18a S1 0.0038 0.18a S2 0.0326 S2 0.0062 S2 0.0075 CC 0.0048b CC 0.0018b CC 0.0009b 2–4% S1 0.0067 0.18a S1 0.0011 0.18a S1 0.0017 0.18a S2 0.0134 S2 0.0022 S2 0.0034 CC 0c CC 0c CC 0c 4–8% S1 0.0058 0.18a S1 0 0d S1 0 0d S2 0.0117 S2 0 S2 0 a Assumes one female per redd with an average size of 5.4 m2. b Usable fraction values for CC apply only to the section downstream of the Middle Yuba River confluence. A spawning capacity of zero was applied in the model in the reach upstream of the Middle Yuba River confluence. c Spawning habitat was not present in channel gradients ≥ 4% in surveys of the NBB sub-basin (i.e., current conditions) (Nikirk and Mesick 2006). d Assumes spawning does not occur in riffles or runs with channel gradients ≥ 4%.

February 2012 Stillwater Sciences F-3 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

REARING

Table F-6. Spring-run Chinook salmon juvenile summer rearing density and usable fraction values for each habitat type and channel gradient combination used to parameterize the RIPPLE HAB module for all sub-basins and scenarios.

Pool Riffle Run Channel gradient Density Usable Density Usable Density Usable (fish/m2)a fraction2 (fish/m2)a fraction2 (fish/m2)a fractionb 0–1% 2.829 1 0.395 1 1.711 1 1–2% 0.772 1 0.108 1 0.467 1 2–4% 0.772 0.75 0.108 0.75 0.467 0.75 4–8% 0.772 0.25 0.108 0.25 0.467 0.25

a Juvenile spring-run Chinook salmon densities reported by Everest and Chapman (1972) (1.8 fish/m2 and 0.5 fish/m2 in 0-1% and 1-2% gradients, respectively) were apportioned by habitat type in proportion to mean habitat-specific (i.e., pool, riffle, and run) densities of juvenile spring-run Chinook salmon in 22 Idaho streams reported by Bjornn and Reiser (1991) (mean pool densities = 0.215 fish/m2; mean riffle densities = 0.030 fish/m2; mean run densities = 0.130 fish/m2). b The 2–4% and 4–8% gradient classes were parameterized with the same density values as the 1–2% gradient class, but usable fractions were lowered to 0.75 and 0.25, respectively, to reflect the lower carrying capacity expected at higher gradients. Juvenile rearing densities and usable fractions were not changed between model scenarios.

February 2012 Stillwater Sciences F-4

Appendix G

Spring-run Chinook Salmon POP Module Methods and Tables

mortality was e Middle Yuba

Stillwater Sciences r each age class were based on on age class were based each r lues of smolt-0-sized juvenile of smolt-0-sized lues juvenile of smolt-1-sized lues and the relationship between the relationship and e Butte Creek data included included data e Butte Creek adjusted were class age for each urements in th in urements Figure 25) indicates that this that this indicates Figure 25) ected in Butte Creek from 2001– from Creek in Butte ected Outmigrant trapping data from trapping Outmigrant An additional 5% man and Nimbus hatcheries from from hatcheries man and Nimbus ngth regression developed by by developed regression ngth ather River Hatchery from 1967– Hatchery ather River with moderatelycool water with wire-tagged spring-run Chinook spring-run wire-tagged (Tagart 1976, McCuddin 1977).

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run Percent of spawning run in each age class returning to the Feather Feather the to returning class age each in run of spawning Percent al. 2009). et (Cavallo River hatchery observed 5% mortalityon pre-spawn mortality was imposed based year in 2004, a in Butte Creek al. 2006). (Ward et temperatures addedas estimate an of mortalitytodue predation and poachingof judgment. professional on adults, based coded- Based on sex ratio of Demko 1997). The and (Cramer River hatchery Feather entering Hatchery River Feather the at classes age of all female fraction et al. 2009). (Cavallo from 1997–2006 was 0.455 fecundityCalculated from vs. le data fo CDFG (1998a,b). Fork length code-wire tagged individuals coll code-wire tagged individuals 2004 (McReynolds et al. 2005). Th 2004 (McReynoldsal. 2005). et males and females, so fork lengths females. of size smaller the reflect accurately downward to more Chinook spring-run that reports (2009) Cavallo For comparison, since hatchery River Feather the at spawned artificially salmon female. eggs per 5,300 of average an 1997 have produced Based approximately on survival va on Based approximately permeabilitysurvival and Chinook salmon released at Cole released Chinook salmon 1968–1970 (Reisenbichler et al. 1982). survival va on Based approximately at Fe released Chinook salmon et al. 1982). (Reisenbichler 1955 in Hatchery 1970 and Nimbus permeability meas Based on gravel (UYRSPST 2007) and South Yuba Based on professional judgment. Based on professional Butte Creek from 2003–2004 indicate that approximately 93% of 93% of that approximately 2003–2004 indicate from Butte Creek (McRenyolds emergence after soon migrated captured outmigrants et al. (2004, Lindley al. 2005). et creeks. and Deer Mill lower for considerably is value

Watershed Yuba River in the Upper 0.90 0.01 0.05 0.76 0.75 MY, NY, & NBB = SY = 0.54 SY = 0.54 module for each Chinook salmon model run. model salmon Chinook each module for G-1 del Value selecting value for Sources/rationale and winter) and winter) and that survive from the from survive that . esmolt0 gence (late fall gence (late smolt1 or s that survive from spawning until s that survive from t population that survives during survives during that population t that survive from Englebright Dam to survive from Englebright Dam that to survive from Englebright Dam that ng population comprised of females. of females. comprised population ng of females. comprised population ng of females. comprised population ng of females. comprised population ng 0.10 0.55 0.60 0.60 ) fry into those migrating out of the Upper those migrating out of into fry ) smolt0 smolt0 smolt1 ning run comprised of age-2 fish comprised of age-2 ning run fish comprised of age-3 ning run fish comprised of age-4 ning run fish comprised of age-5 ning run 0.11 0.47 0.41 0.01 swimup Biological parameters input into the POP input parameters Biological Table G-1. holding in freshwater. freshwater. holding in Determines fraction of the adul of Determines fraction Partitions emergent ( Partitions emergent estuary until adult return to freshwater. to freshwater. return adult until estuary Determines fraction of Determines fraction of and fraction freshwater to adult return of Determines fraction freshwater. to return adult individual of Determines fraction redd gravels. from emergence Yuba River watershed soon after emer watershed soon after Yuba River those remaining to become those remaining

a a

a b Parameter Parameter used in mo parameter of how Description to adult survival adult to survival adult to fraction fraction

Technical Report Technical February 2012 Smolt0 Smolt1 Spawning fraction 2 Spawning fraction 3 Spawning fraction 4 Spawning fraction 5 adult spaw of Fraction adult spaw of Fraction adult spaw of Fraction Holding survival adult spaw of Fraction female 2 Fraction female 3 Fraction female 4 Fraction female 5 Fraction of the age-2 Fraction spawni Eggs per female 2 of the age-3 Fraction spawni Eggs per female 3 of the age-4 Fraction spawni Eggs per female 4 of the age-5 Fraction spawni age-2 spawners age-3 spawners Eggs per female 5 age-4 spawners age-5 spawners survival Embryo Efry 1,000 4,000 6,000 8,500

. efry

Stillwater Sciences the “0-age inactive” life stage. the “0-age inactive” lue is intermediate between between intermediate lue is e value is the same as that same as is the e value e value is the same as that same as is the e value for "0-age resident rearing." rearing." for "0-age resident estuary and ocean survival of and ocean estuary to adult survival) for survival) to adult smolt0 ent relationship applied in the RIPPLE POP the in applied ent relationship

Modeling Spring-Run Chinook Salmon and Steelhead and Chinook Salmon Modeling Spring-Run Based on professional judgment. Th Based on professional al. (2004) Lestelle et by reported Based on professional judgment. Th Based on professional for al. (2004) Lestelle et by reported Based on professional judgment. Va Based on professional values survival rearing" transient and "0-age colonization" "fry al. (2004). Lestelle et by reported Based on the mean of 7 years of survival estimates (0.0027) from survival years of the mean of 7 Based on ocean the in capture to Dam Diversion Red Bluff at fry of release results of 0.27 a value Using 2001). and McClain (Brandes fishery delta, river, lower combined in a 0.01 * 0.0027 (0.27

Watershed Yuba River in the Upper 0.70 0.70 0.50 0.27 ed for in the stock-recruitm in ed for G-2 del Value selecting value for Sources/rationale ) juvenile population that ) juvenile population efry position. Superimposition is account position. Superimposition ummering age 0 juvenile population age 0 ummering per Yuba channel network at Yuba channel per that survive during the period from period the during that survive in that survive during time spent in the the in spent time during survive that in efry efry mortality such as predation or disease. disease. or predation as such mortality . . smolt1 Determines fraction of Determines fraction emergence until leaving the Up the leaving until emergence Englebright Dam. Englebright survives during the period from emergence until outmigration of emergence until outmigration from the period survives during smolt0 Determines fraction of the resident (non- the resident of Determines fraction Determines fraction of Determines fraction the ocean. entering prior to delta and river lower Sacramento the overs of Determines fraction that survives during the period from early summer until outmigration from period the that survives during as

a

a

a

survival survival survival winter1 efry to

a to esmolt0 Parameter Parameter used in mo parameter of how Description summer0 to to to

Technical Report Technical February 2012 module. Survival values account for density-independent for account Survival values superim not redd but mortality density-independent Accounts for survival Swimup Efry Fry Summer0 a

b Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

REFERENCES

Brandes, P. L., and J. S. McLain. 2001. Juvenile Chinook salmon abundance, distribution, and survival in the Sacramento-San Joaquin estuary. Pages 39–138 in R. L. Brown, editor. Contributions to the biology of Central Valley salmonids. Fish Bulletin 179: Volume 2. California Department of Fish and Game, Sacramento.

Cavallo, B., R. Brown, and D. Lee. 2009. Hatchery and Genetic Management Plan for Feather River Hatchery Spring-run Chinook Salmon Program. Prepared by Cramer Fish Sciences, Auburn, California for California Department of Water Resources, Sacramento, California.

CDFG (California Department of Fish and Game). 1998a. Central Valley anadromous fish-habitat evaluations: October 1996 through September 1997. Stream Evaluation Program, Technical Report No. 98-4. Prepared by CDFG, Environmental Services Division, Stream Flow and Habitat Evaluation Program for U. S. Fish and Wildlife Service, Central Valley Anadromous Fish Restoration Program.

CDFG. 1998b. A status review of the spring-run Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento River drainage. Report to the Fish and Game Commission, Candidate Species Status Report 98-01. CDFG, Sacramento.

Cramer, S. P., and D. B. Demko. 1997. The status of late-fall and spring chinook salmon in the Sacramento River basin regarding the Endangered Species Act. Special Report. Submitted to National Marine Fisheries Service on behalf of Association of California Water Agencies and California Urban Water Agencies. Prepared by S. P. Cramer and Associates, Inc., Gresham, Oregon.

Lestelle, L. C., L. E. Mobrand, and W. E. McConnaha. 2004. Information structure of Ecosystem Diagnosis and Treatment (EDT) and habitat rating rules for Chinook salmon, coho salmon, and steelhead trout. Prepared by Mobrand Biometrics, Inc., Vashon Island, Washington.

Lindley, S. T., R. Schick, B. P. May, J. J. Anderson, S. Greene, C. Hanson, A. Low, D. McEwan, R. B. MacFarlane, C. Swanson, and J. G. Williams. 2004. Population structure of threatened and endangered Chinook salmon ESUs in California's Central Valley Basin. Technical Memorandum NOAA-TM-NMFS-SWFSC-360. National Marine Fisheries Service, Southwest Fisheries Science Center.

McReynolds, T. R., C. E. Garman, P. D. Ward, and M. C. Schommer. 2005. Butte and Big Chico creeks spring-run Chinook salmon, Oncorhynchus tshawytscha, life history investigation 2003- 2004. Inland Fisheries Administrative Report No. 2005-1. California Department of Fish and Game, Sacramento Valley and Central Sierra Region, Rancho Cordova.

Reisenbichler, R. R., J. D. McIntyre, and R. J. Hallock. 1982. Relation between size of Chinook salmon, Oncorhynchus tshawytscha, released at hatcheries and returns to hatcheries and ocean fisheries. California Fish and Game 68: 57–59.

UYRSPST (Upper Yuba River Studies Program Study Team). 2007. Upper Yuba River watershed Chinook salmon and steelhead habitat assessment. Technical Report. Prepared by

February 2012 Stillwater Sciences G-3 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Upper Yuba River Studies Program Study Team for California Department of Water Resources, Sacramento, California.

Ward, P. D., T. R. McReynolds, and C. E. Garman. 2006. Butte Creek spring-run Chinook salmon, Oncorhynchus tshawytscha, pre-spawn mortality investigation 2004. Administrative report no. 2006-1. California Department of Fish and Game, Inland Fisheries, Sacramento, California.

February 2012 Stillwater Sciences G-4

Appendix H

Steelhead HAB Module Methods and Tables

Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

SPAWNING DENSITY AND USABLE FRACTION

Table H-1. Values used to parameterize the RIPPLE HAB module for steelhead female spawning density and fraction of the channel usable for spawning for each habitat type and channel gradient combination in the SY, MY, and NY model runs. The same values were used for each model scenario. It was assumed that spawning does not occur in cascade habitats. Pool Riffle Run Channel Model Density Model Density Model Density Usable Usable Usable gradient sub- (females sub- (females sub- (females fraction fraction fraction basin /m2) basin /m2) basin /m2) SY 0.0213 SY 0.0064 SY 0.0043 0–1% MY 0.0216 0.50a MY 0.0054 0.50a MY 0.0041 0.50a NY 0.0215 NY 0.0059 NY 0.0042 SY 0.0146 SY 0.0028 SY 0.0034 a a a 1–2% MY 0.0237 0.50 MY 0.0046 0.50 MY 0.0054 0.50 NY 0.0187 NY 0.0036 NY 0.0043 SY 0.0061 SY 0.0009 SY 0.0024 b b b 2–4% MY 0.0092 0.66 MY 0.0017 0.66 MY 0.0018 0.66 NY 0.0075 NY 0.0012 NY 0.0019 SY 0.0036 SY 0 SY 0 4–8% MY 0.0115 0.66b MY 0 0c MY 0 0c NY 0.0074 NY 0 NY 0 a Assumes one female per redd with a mean size of 2.0 m2 (Hannon and Deason 2007). b Assumes one female per redd with a mean size of 1.5 m2 (Trush 1991). c Assumes spawning does not occur in riffles or runs with channel gradients ≥ 4%

Table H-2. Values used to parameterize the RIPPLE HAB module for steelhead female spawning density and usable fraction of spawning for each habitat type and channel gradient combination in the NBB model runs for Current Conditions (CC), Scenario 1 (S1), and Scenario 2 (S2). It was assumed that spawning does not occur in cascade habitats. Pool Riffle Run Channel Density Density Density Usable Usable Usable gradient Scenario (females Scenario (females Scenario (females fraction fraction fraction /m2) /m2) /m2) CC 0.0025 CC 0.0009 CC 0.0004 0–1% S1 0.0107 0.50a S1 0.0030 0.50a S1 0.0021 0.50a S2 0.0215 S2 0.0059 S2 0.0042 CC 0.0012 CC 0.0004 CC 0.0002 1–2% S1 0.0093 0.50a S1 0.0018 0.50a S1 0.0022 0.50a S2 0.0187 S2 0.0036 S2 0.0043 CC 0.0021 CC 0.0008 CC 0.0004 2–4% S1 0.0038 0.66b S1 0.0006 0.66b S1 0.0009 0.66b S2 0.0075 S2 0.0012 S2 0.0019 CC 0c CC 0d CC 0d 4–8% S1 0.0037 0.66b S1 0d 0 S1 0d 0 S2 0.0074 S2 0d S2 0d a Assumes one female per redd with a mean size of 2.0 m2 (Hannon and Deason 2007). b Assumes one female per redd with a mean size of 1.5 m2 (Trush 1991). c Spawning habitat was not present in channel gradients ≥ 4% in surveys of the NBB sub-basin (i.e., current conditions) (Nikirk and Mesick 2006). d Assumes spawning does not occur in riffles or runs with channel gradients ≥ 4%

February 2012 Stillwater Sciences H-1 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

SUMMER JUVENILE REARING DENSITY AND USABLE FRACTION

Table H-3. Steelhead age 1+ summer rearing density and usable fraction values for each habitat type and channel gradient combination used to parameterize the RIPPLE HAB module for all sub-basins and scenarios. Pool Riffle Run Channel gradient Density Usable Density Usable Density Usable (fish/m2) fraction (fish/m2) fraction (fish/m2) fraction 0–1%a 0.085 1 0.157 1 0.149 1 1–2%a 0.085 1 0.157 1 0.149 1

2–4%b 0.104 1 0.044 1 0.037 1

4–8%b 0.104 1 0.044 1 0.037 1

8–12%b 0.104 1 0.044 1 0.037 1

a The mean of age 1+ steelhead summer densities calculated from NID and PG&E (2009) electrofishing data (0.121 fish/m2) was apportioned by habitat type in proportion to mean habitat-specific density values of 4-8 in O. mykiss calculated from Gast et al. (2005) snorkel data for the South and Middle Yuba rivers (mean of pool densities = 0.013 fish/m2; mean riffle densities = 0.023 fish/m2; mean run densities = 0.022 fish/m2). b The mean of age 1+ O. mykiss summer densities reported for pools, riffles, and runs in tributary streams in northern California (Upper Penitencia Creek [Stillwater Sciences 2006d], Devil’s Gulch [Stillwater Sciences 2008], tributaries to the South Fork Eel and Mattole rivers [Connor 1996]) and tributaries to the South Umpqua River, Oregon (Scarnecchia and Roper 2000) were used to parameterize channels with gradients ≥ 2%.

WINTER JUVENILE REARING DENSITY AND USABLE FRACTION

As described in Section 7.2.1.4 usable fraction parameter values were calculated based on observed substrate composition in each sub-basin. Dominant and subdominant substrate data collected in the upper Yuba River watershed (Stillwater Sciences 2006a; K. Peacock, HDR|DTA, Bellingham, Washington, unpubl. data, provided 1 December 2010) were categorized into qualitative categories of “good,” “fair,” and “poor” habitat (Table H-4). Then, for the SY and MY sub-basins (combined data), the fraction of stream length containing substrates in these categories was calculated for each gradient class, except in the NBB sub-basin, where gradient-specific data were not available (Table H-5).

The fraction of stream length comprised of good, fair, and poor habitats in each sub-basin was then scaled by the fraction of the area of good, fair, and poor habitats assumed to be suitable for winter rearing (Table H-5) to determine the contribution of each to the total. We assumed that stream reaches with “good” habitat had a usable fraction 0.75 and adjusted usable fraction of “fair” and “poor” categories downward to 0.45 and 0.03 in accordance with the relative juvenile steelhead densities measured in winter habitats of similar quality by Meyer and Griffith (1997). Finally, the overall usable fraction for each gradient class was calculated by summing the contribution of good, fair, and poor (Table H-5). Table H-6 shows the age 1+ juvenile steelhead winter densities and usable fraction values used to parameterize the RIPPLE HAB module for each sub-basin. The same values were used for all scenarios.

February 2012 Stillwater Sciences H-2 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table H-4. Dominant and subdominant substrate combinations used to assign “good,” “fair,” and “poor” winter habitat quality categories to each stream reach.

Good Fair Poor Boulder dominant with Boulder dominant and Gravel or smaller gravel or smaller cobble subdominant dominant subdominant Cobble dominant with Cobble dominant and gravel or smaller boulder subdominant subdominant Bedrock dominant Boulder dominant and Cobble dominant and bedrock subdominant bedrock subdominant

Table H-5. Fraction of each winter habitat quality category present in the SY, MY, and NBB sub-basins by gradient class and contribution of each to total usable fraction. Fraction of stream length Contribution to total Sub- Channel containing each category Total usable basin gradient fractiond Good Fair Poor Gooda Fairb Poorc 0–1% 0.428 0.205 0.367 0.321 0.092 0.013 0.426 SY 1–2% 0.526 0.124 0.350 0.395 0.056 0.012 0.462 and 2–4% 0.685 0.050 0.264 0.514 0.023 0.009 0.546 e MY 4–8% 0.707 0.037 0.256 0.530 0.016 0.009 0.555 8–12% 0.793 0.000 0.207 0.595 0.000 0.007 0.602 NBBf,g All 0.367 0.426 0.000 0.573 0.042 0.005 0.621 a Assumed 75% of channels categorized as “good” was usable for winter rearing. b Assumed 45% channels categorized as “fair” was usable for winter rearing. c Assumed 3% channels categorized as “poor” was usable for winter rearing. d Sum of good, fair, and poor. e Source: (Stillwater Sciences 2006a) f Source: (K. Peacock, HDR|DTA, Bellingham, Washington, unpubl. data provided 1 December )2010 g Gradient-specific substrate data were not available.

February 2012 Stillwater Sciences H-3 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed

Table H-6. Age 1+ juvenile steelhead winter densities and usable fraction values used to parameterize the RIPPLE HAB module for each habitat type and channel gradient combination for each sub-basin. The same values were used for all model scenarios.a Pool Riffle Run Channel Sub- gradient basin Density Usable Density Usable Density Usable (fish/m2)a fraction (fish/m2)a fraction (fish/m2)a fraction SY, MY, 0.426 0.426 0.426 0–1% NYb 5.5 5.5 5.5 NBB 0.621 0.621 0.621 SY, MY, 0.462 0.46 0.46 1–2% NYb 5.5 5.5 5.5 NBB 0.621 0.621 0.621 SY, MY, 0.546 0.546 0.546 2–4% NYb 5.5 5.5 5.5 NBB 0.621 0.621 0.621 SY, MY, 0.555 0.555 0.555 4–8% NYb 5.5 5.5 5.5 NBB 0.621 0.621 0.621 SY, MY, 0.602 0.602 0.602 8–12% NYb 5.5 5.5 5.5 NBB 0.621 0.621 0.621 a Source: Meyer and Griffith (1997). b NY sub-basin values were parameterized based on data collected in the SY and MY sub-basins. D50 data collected in the NY (see Appendix E) suggest that the sub-basin contains a high fraction of unembedded cobble and boulder substrate and can be expected to have winter habitat quality as good as or better than the SY and MY sub-basins.

February 2012 Stillwater Sciences H-4