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ASSESSING FLOWS FOR FISH BELOW

A SYSTEMATIC APPROACH TO EVALUATE COMPLIANCE WITH FISH AND GAME CODE 5937

THEODORE E. GRANTHAM PETER B. MOYLE CENTER FOR WATERSHED SCIENCES UNIVERSITY OF CALIFORNIA, DAVIS ONE SHIELDS AVENUE DAVIS, CA 95616

October 22, 2014*

*Revised Dec. 15, 2014 (See Erratum) This report was prepared by:

Theodore E. Grantham and Peter B. Moyle Center for Watershed Sciences University of California, Davis One Shields Avenue Davis, CA 95616

Corresponding author: Theodore (Ted) Grantham [email protected]

Copyright ©2014 The Regents of the University of California

All rights reserved

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Please cite this report as:

Grantham, T. E. and P. B. Moyle. 2014. Assessing flows for fish below dams: a systematic approach to evaluate compliance of California’s dams with Fish and Game Code Section 5937. Center for Watershed Sciences Technical Report (CWS-2014-01), University of California, Davis. 106 p. ii

TABLE OF CONTENTS

Tables ...... v Figures ...... vi Acknowledgements ...... ix Executive Summary ...... x Introduction ...... 1 Effects of dams on California’s rivers ...... 2 Effects of dams on California’s fish populations ...... 4 Section 5937 and ‘fish in good condition’ ...... 6 Applying Section 5937 to restore flows below dams ...... 8 A systematic approach for evaluating dams ...... 10 Methods ...... 13 Step 1. Building a database ...... 13 Step 2. Assessing flow regime alteration below dams ...... 15 Step 3. Assessing condition of native fish below dams ...... 16 Step 4. Identifying regulatory considerations ...... 18 Step 5. Identifying and ranking candidate dams ...... 18 Step 6. Preliminary case study investigations ...... 20 Evaluation Results ...... 21 Flow regime alteration below dams ...... 22 Indicators of fish condition ...... 30 Relationships between hydrologic alteration and fish condition ...... 33 Dams subject to federal environmental flow requirements ...... 36 Identification and ranking of candidate dams ...... 37 Preliminary site investigations ...... 44 Discussion ...... 48 Systematic evaluation of dams ...... 48 Limitations ...... 49 Recommendations ...... 50 Case Studies ...... 52 Case study 1: Black Butte Dam ...... 53 Hydrologic Conditions ...... 55 iii

Condition of Downstream Fish Populations ...... 56 Management of Downstream Flows for Fish ...... 57 Case study 2: Conn Creek Dam...... 58 Hydrologic Conditions ...... 60 Condition of Downstream Fish Populations ...... 61 Management of Downstream Flows for Fish ...... 61 Case study 3: Peters Dam ...... 62 Hydrologic Conditions ...... 64 Condition of Downstream Fish Populations ...... 65 Management of Downstream Flows for Fish ...... 65 Case study 4: Woodbridge Diversion Dam ...... 67 Hydrologic Conditions ...... 69 Condition of Downstream Fish Populations ...... 71 Management of Downstream Flows for Fish ...... 72 Case study 5. Twitchell Dam ...... 73 Hydrologic Conditions ...... 75 Condition of Downstream Fish Populations ...... 75 Management of Downstream Flows for Fish ...... 76 Case study 6. Long Valley Dam ...... 77 Hydrologic Conditions ...... 79 Condition of Downstream Fish Populations ...... 79 Management of Downstream Flows for Fish ...... 80 Case study 7. Casitas Dam ...... 81 Hydrologic Conditions ...... 83 Condition of Downstream Fish Populations ...... 84 Management of Downstream Flows for Fish ...... 84 Case study 8. Boles Meadow Dam ...... 85 Hydrologic Conditions ...... 87 Condition of Downstream Fish Populations ...... 87 Management of Downstream Flows for Fish ...... 88 Case study 9. ...... 89 Hydrologic Conditions ...... 91 Condition of Downstream Fish Populations ...... 92 iv

Management of Downstream Flows for Fish ...... 90 Case study 10. Dwinnell Dam ...... 91 Hydrologic Conditions ...... 93 Condition of Downstream Fish Populations ...... 93 Management of Downstream Flows for Fish ...... 94 Case study findings ...... 95 References ...... 97 Appendix A ...... 105 Sensitive native fish species list ...... 105 Appendix B ...... 110 List of dams evaluated ...... 110 Appendix C ...... 127 Model performance evaluation ...... 129 Appendix D ...... 134 FERC-regulated dams ...... 134

Erratum……………………………………………………………………………………………………………143 v

TABLES

Table 1. Top 20-ranking dams sorted by storage capacity and seasonal flow deviation ...... 40

Table 2. Top 20-ranking dams sorted by native species richness and sensitive species richness ...... 42

Table 3. Top 20-ranking dams sorted by ESA-listed salmon and steelhead trout populations ...... 44

Table 4. Case study dams ...... 46

Table 5. Black Butte Dam on Stony Creek, Tehama County ...... 56

Table 6. Conn Creek Dam on Conn Creek, Napa County ...... 61

Table 7. Peters Dam on Lagunitas Creek, Marin County ...... 64

Table 8. Woodbridge Diversion Dam on the , San Joaquin County ...... 70

Table 9. Twitchell Dam on the Cuyama River, San Luis Obispo and Santa Barbara counties ...... 75

Table 10. Long Valley Dam on the Owens River, Mono County ...... 79

Table 11. Casitas Dam on Coyote Creek, Ventura County ...... 83

Table 12. Boles Creek Dam on Boles Creek, Modoc County...... 87

Table 13. Pine Flat Dam on the , Fresno County...... 91

Table 14. Dwinnell Dam on the Shasta River, Siskiyou County...... 94

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FIGURES

Figure 1. Dams in California ...... 1

Figure 2. Pre-dam and post-dam mean monthly flows for the at Fair Oaks (USGS gage #1144650) ...... 3

Figure 3. Conceptual diagram of dam evaluation approach ...... 11

Figure 4. Evaluation approach and criteria for identifying dams where improved downstream flows may be warranted for Section 5937 compliance ...... 14

Figure 5. Dams evaluated in California (n =753) with frequency distributions of dam height, storage capacity, and upstream catchment areas ...... 21

Figure 6. Histograms of observed/expected mean monthly flows for all gaged dams. O/E values between 0.75-1.25 (gray bars) indicate that observed flows are similar to expected values ...... 23

Figure 7. Histogram of observed/expected maximum 1-day discharge. O/E values near 1 (gray bar) indicate that observed flows are similar to expected values ...... 24

Figure 8. Histogram of correlation coefficient between observed and expected monthly flows, for all gages below dams. Gray bar denotes high correlation, or strong correspondence, between observed and expected seasonal monthly flow patterns ...... 25

Figure 9. Examples of seasonal flow alteration below dams, as measured by correlation between expected (modeled unimpaired) and observed mean monthly flows...... 26

Figure 10. Impounded runoff (IR) ratio for dams in California, representing the capacity relative to the (modeled) mean annual inflow; inset map illustrates the difference between IR and CIR for series of dams on the ...... 27

Figure 11. Relationship between O/E monthly flows, O/E maximum 1-day flows, Pearson’s r and the cumulative impounded runoff (CIR) ratio at gaged dams ...... 29

Figure 12. Patterns of species loss from HUC12 watersheds for 28 native fish species with historical and current range data ...... 30

Figure 13. Patterns of sensitive species richness within California’s HUC12 watersheds; population status of each native species based on Moyle et al. 2011 ...... 31

Figure 14. Current distribution of anadromous salmonid species, listed as threatened or endangered under the federal Endangered Species Act ...... 332

Figure 15. Native species richness plotted against annual discharge and cumulative storage ...... 33

Figure 16. Number of sensitive species plus species losses, plotted against annual discharge and cumulative storage capacity ...... 34

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Figure 17. Number of sensitive species plus species losses, plotted against impounded runoff (IR), cumulative impounded runoff, monthly flow deviation, maximum 1-day flow deviation, and seasonal flow deviation; flow deviation metrics are transformed: increasing values (from 0) indicate increasing degree of deviation from modeled unimpaired conditions ...... 35

Figure 18. Dams with (gray, n = 165) and without (black, n = 588) known federal environmental flow requirements ...... 36

Figure 19. High priority candidate dams (n = 220) for assessing compliance with Section 5937 ...... 37

Figure 20. Ten case study dams from the list of candidate dams (n = 220), selected to provide preliminary site investigation of the potential effects of dam operations on downstream fish ...... 46

Figure 21. Black Butte Dam and catchment (1,916 km2) on Stony Creek. Downstream flows were evaluated at USGS gage #11388000 below the dam ...... 53

Figure 22. Expected (E, modeled) and observed (O) mean monthly flows below Black Butte Dam and the O/E ratio ...... 56

Figure 23. Conn Creek Dam and catchment on Conn Creek, a tributary to Napa Creek in Sonoma County. Downstream flows were evaluated at USGS gage #11456500 ...... 58

Figure 24. Peters Dam and upstream catchment (267 km2) on Lagunitas Creek in Marin County. Downstream Flows were evaluated at USGS gage #11460400 ...... 62

Figure 25. Expected (E, modeled) and observed monthly flow below Peters Dam on Lagunitas Creek ...... 64

Figure 26. Woodbridge Diversion Dam and catchment (1,682 km2) on the Mokelumne River, San Joaquin County; inset map shows large upstream dams and USGS gages above the dams (#11319500), below Camanche Dam (#11323500), and below Woodbridge Dam (#11325500) ...... 67

Figure 27. Observed daily discharge in the Mokelumne River for the 2010 water year, above Pardee Dam, downstream of Camanche Dam, and below Woodbridge Dam ...... 71

Figure 28. Expected (E, modeled) and observed mean monthly flow below Woodbridge Dam on the Mokelumne River ...... 72

Figure 29. Twitchell Dam and catchment (2,888 km2) on the Cuyama River, in southern San Luis Obispo and northern Santa Barbara counties ...... 73

Figure 30. Long Valley Dam and catchment (994 km2) on the Owen River, Mono County ...... 77

Figure 31. Casitas Dam and catchment (105 km2) on Coyote Creek, a tributary to the Ventura River, Ventura County ...... 81

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Figure 32. Mean monthly flows on Coyote Creek before and after construction of Casitas Dam, assessed at USGS gage #11118000 ...... 83

Figure 33. Boles Meadow dam and catchment (692 km2) on Boles Creek, Modoc County ...... 85

Figure 34. Pine Flat Dam and catchment (4,000 km2) on the Kings River in Fresno County. Flows were evaluated at USGS gage #11221500 ...... 90

Figure 35. Expected (E, modeled) and observed mean monthly flows below Pine Flat Dam on the Kings River...... 91

Figure 36. Dwinnell Dam and catchment (142 km2) on the Shasta River, Siskiyou County ...... 93

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ACKNOWLEDGEMENTS

Many people have contributed to this report. The development of the evaluation approach benefited greatly from conversations with Curtis Knight, Monty Schmitt, Brian Johnson, and Rene Henery, who offered a broad range of expertise pertaining to the management of dams and their impacts to California’s river ecosystems. We received excellent support from researchers at the University of California – Davis Center for Watershed Sciences. In particular, Josh Viers, Nick Santos, and Jacob Katz were instrumental in the development and analysis of the PISCES database. Eric and Sarah Yarnell also provided helpful feedback and research support. Sydney Vickery assisted with figure development and Chris Bowman provided valuable editorial advice. We thank Daren Carlisle and David Wolock for technical guidance on hydrologic modeling. Additional helpful discussion and assistance with data sources came from Marshall Olin, Chandra Ferrari, Joe Merz, Jonathan Koehler, Steve Parmenter, Dale Mitchell, Greg Andrew, Stuart Reid, Darren Mierau, Mark Drew, Gordon Becker, Matt Kondolf, Larry Brown and Jeff Thompson. This research was supported with funding from the Natural Resources Defense Council, California Trout and Trout Unlimited. We alone are responsible for the analysis, results and recommendations of this report and any errors herein.

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EXECUTIVE SUMMARY

There are thousands of dams in California, most of which were built and are operated for water supply and flood protection benefits with little consideration for their effects on fish. For more than 100 years, however, the State of California has legally recognized the need to ensure that adequate flows are released below dams to maintain fish in good condition. In the early 20th century, Fish and Game Code 5937 was adopted, which states that the “owner of any dam shall allow sufficient water at all times…to pass over, around, or through the dam, to keep in good condition any fish that may be planted or exist below the dam.” Despite the clear language and intent of Section 5937 to protect fish below dams, dam owners have generally not met this requirement and the state agencies charged with its implementation have not enforced it. However, successful lawsuits since the 1970s have applied Section 5937 on several regulated rivers to improve flows for fish and wildlife, and indicate that there is an for broader implementation of environmental flows in California’s rivers and streams.

Sections 5937’s legal requirement to ensure adequate flows for fish potentially applies to thousands of dams in California. However, determining which dams may not be in compliance with the code is a daunting task that state agencies have not undertaken to date. There remains a need for a systematic assessment of dams to ensure uniform and balanced implementation of Section 5937 flow protections throughout California. Such flow protections are critical to the preservation of California’s native fish species and fishery resources, which are severely threatened by river ecosystem degradation, human population growth and climate change.

This technical report presents an evaluation approach to identify dams in California where flow modifications and/or other management actions may be warranted to comply with Section 5937. The approach follows a tiered framework that focuses on the inventory, characterization, and selection of dams based on evidence of flow regime alteration and downstream fish community impairment. First, a database of dams is compiled and used to define the distribution and characteristics of California dams. Next, hydrologic conditions below dams are assessed to quantify the extent to which flows may deviate from natural, unimpaired conditions. The condition of native fish in proximity to each dam is then evaluated based on range maps and population status. Indicators of fish condition impairment were assessed in the sub-watersheds within which dams were located and included (1) the loss of native fish species based on their historic range and (2) the presence of native fish species considered at risk of extinction. All dams associated with evidence of hydrologic alteration and indicators of fish condition impairment were then identified and ranked. Finally, a series of case studies were selected from the list of dams potentially in need of improved environmental flows to provide diverse, site-specific examples of how dam operations may be affecting the condition of downstream fish.

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Following an initial evaluation of more than 1,400 large dams in California, this analysis focused on 753 dams that are likely subject to Section 5937 flow requirements. These dams occur within a broad range of biogeographic settings and represent a diversity of sizes and operational purposes. They are distributed throughout the state, but occur in highest density in the , central and Coast Ranges, and the upper Klamath River Basin. There are relatively few qualifying dams in the north coast region of California, which has a dense network of rivers, and in the southeastern region of the state where few rivers are present.

There is evidence that many of the dams evaluated have potential to alter downstream flow regimes. About 350 dams have storage capacities large enough to capture more than 50% of annual river inflow. Reservoir storage capacity was equal or greater than total annual inflow for 178 dams. For dams with downstream flow gages (about 200), there was evidence of substantial flow regime alteration. For the vast majority of gaged dams, observed flows deviated from expected natural patterns by at least 50% for at least six months of the year. In addition, for more than half of the gaged dams evaluated, maximum 1-day flows were less than 50% of predicted values. Although several dams appear to have substantially altered seasonal flow patterns (assessed by correlation between observed and expected monthly flows), flow seasonality has been largely preserved below most gaged dams.

About 400 of the 753 dams evaluated are within the range of at least one sensitive fish species (i.e., those with vulnerable or threatened population status), including more than 200 within the range of anadromous salmonids listed under the federal Endangered Species Act. There are an additional 250 dams located in watersheds that have lost at least one native species based on their historic ranges. A comprehensive, statistical analysis of the relationships between dam-related flow alteration and fish condition was beyond the scope of this study. There was, however, some evidence that the number of sensitive species and species losses is associated with hydrologic alteration below dams. For example, dams with no sensitive species or losses were generally associated with the lowest degree of hydrologic alteration, based on impounded runoff, cumulative impounded runoff, and maximum 1-day flow deviation metrics. The association of dams with indicators of biological impairment is not causal evidence that dam operations are responsible for the poor condition of fish. However, a large body of literature documenting the impacts of dams on fish assemblages strongly suggests that dam operations remain an important threat to the persistence of California’s native fish populations.

From an initial list of more than 1,400 dams, 220 were identified as high-priority sites to further assess the condition of fish based on evidence of hydrologic and biological impairment. These dams were then ranked and sorted based on their physical features (reservoir capacity), hydrologic indicators (degree of seasonal flow alteration), and associated fish community characteristics. High-priority dams with the largest water storage capacities include many of the state’s biggest dams: on the Trinity River, on the , Pine Flat on Kings River, and Folsom

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Dam on the American River. Dams associated with the greatest downstream hydrologic alteration were also identified and ranked. Among the subset of dams with downstream U.S. Geological Survey (USGS) gaging stations, Tinemaha Dam on the Owens River, and Anderson Dam on Coyote Creek, and Calaveras Dam on Calaveras Creek were associated with the greatest alteration to seasonal monthly flow patterns. High-priority dams associated with the greatest richness of native species include Woodbridge Diversion Dam on the Mokelumne River, Nash Dam on a tributary to Stillwater Creek in Shasta County, and a series of three Rubber Dams on lower Creek. The dams associated with the greatest number of native species with sensitive population status included Keswick and Anderson-Cottonwood dams, Woodbridge Diversion Dam, and Nash Dam.

Ten case studies were selected from the list of high-priority candidate dams to provide specific examples of how dam operations may be affecting the downstream fish community. The case study dams were selected to illustrate the diversity of dam types throughout the state, and do not necessarily represent those in greatest need of improved flows for fish. The case study investigations found that indicators of hydrologic alteration and fish population impairment assessed in the systematic evaluation generally corresponded with documented, site-specific environmental effects of dams. In addition, observed downstream flow alteration was generally coupled with significant downstream habitat alteration. Therefore, poor habitat conditions below many dams suggest that improving flows for fish may also require habitat restoration to maintain fish in good condition. Overall, the case studies illustrated that each dam has a unique set of management constraints, jurisdictional issues, and environmental factors that must be addressed in the context of Section 5937. This is probably true of all dams, and we recommend that site-specific analyses presented in the case studies be done for every high-priority dam identified in this investigation.

This investigation revealed inaccurate data a general lack of information on dam operations, downstream flow regimes, and affected fish communities. The vast majority of dams currently have no downstream flow monitoring stations. The state’s inaccurate reporting and tracking of water availability and use (i.e., diversions) significantly impedes management of environmental flows in California’s rivers. In addition, the sporadic availability and quality of fish observations greatly hinders a statewide assessment of the ecological impacts of dams. For this investigation, we used a new geospatial database of California fish distributions to identify fish species associated with dams at the HUC12- watershed scale. However, the spatial association of fish species downstream of specific dams (upon which the selection criteria are based) is not conclusive. We recommend that indicators of fish community impairment (e.g. sensitive species or loss of species from historic range) below dams be confirmed as part of site-specific investigations.

The effects of California dams in downstream flows remains poorly documented. Therefore, this evaluation approach can be improved as new data and modeling tools become available. Additional monitoring data on downstream flows and fish communities could

xiii change the rankings of dams on the high-priority list. New criteria could also be incorporated in the evaluation framework to support the selection and ranking of high- priority dams for further assessment. Information on the relative vulnerability of California’s fish assemblages to climate change is particularly needed for informing environmental flow implementation strategies. The data-driven framework for evaluating dams is a flexible and adaptive way to incorporate new sources of information to guide river management and decision-making.

This investigation represents the first attempt to systematically evaluate the impacts of California’s major dams on native fish species in the context of Section 5937. The study presents evidence indicating that many California dams are not in compliance with Section 5937. Given the rapid decline of California’s fish fauna and pervasive alteration of the state’s river ecosystems, environmental flow protections are critical for conservation of many native fish populations and are likely to become increasingly so in the future. There is an urgent need for the State to develop an approach to evaluate the compliance of existing dams with its laws to protect California’s fish. This initial screening approach identifies dams that likely warrant site-specific studies and offers guidance on implementing environmental flows to comply with Section 5937.

Keywords: environmental flows, water management, regulated rivers, freshwater fishes, biodiversity conservation, dams, Fish and Game Code Section 5937, California

INTRODUCTION | 1

INTRODUCTION

California has thousands of dams, from small earthen barriers that create ponds for local use to megastructures hundreds of feet tall impounding the state’s major water-supply sources. Building dams on California’s free-flowing streams and rivers began in the 1850s, accelerated during the 19th century in response to demands of hydraulic mining and logging, and peaked between 1900 and 1920 with the expansion of irrigated agriculture. Construction of the State’s largest water-supply dams, mostly by the federal government, was concentrated between 1940 and 1970. Today there are more than 1,400 dams that are large enough to fall under state regulations for safety (DWR 2010). In addition, more than 1,700 smaller dams have been inventoried on California’s rivers and streams (CDFW 2012). These dams a on essentially every major river and stream in the state (Figure 1) and collectively impound over 42 million acre feet, equivalent to 60% of the average runoff in California (Mount 1995).

Figure 1 Dams in California

2 | RESTORING FLOWS FOR FISH BELOW DAMS

EFFECTS OF DAMS ON CALIFORNIA’S RIVERS

All dams alter the timing and magnitude of river flows. California’s mediterranean climate is characterized by a distinct wet season, associated with brief, intense storms followed by a prolonged period of seasonal drought. This seasonal pattern of water availability is out-of-phase with human water demands, which increase during the dry season primarily to support irrigated agriculture. California’s climate seasonality thus has been a strong catalyst for reservoir construction (Gasith and Resh 1999). In addition, multi-year droughts are common in California, as are extreme flood events (Cayan et al. 1999), prompting the need for large reservoirs to enhance water-supply reliability and provide flood protection. As a result, one of the most common effects of dams on river flows in California is reduction in magnitude and frequency of high-flow events (Kondolf and Batalla 2005). Stream flows below dams are often augmented in the summer through late fall to support irrigated agriculture and to expand flood retention capacity of reservoirs (Grantham et al. 2012; Singer 2007). “Flattening” of the seasonal flow regime, resulting from decreased high flows and increased base flows, has been observed in the and all its major tributaries (Brown and Bauer 2010), such as the American River (Figure 2).

INTRODUCTION | 3

Figure 2 Pre-dam and post-dam mean monthly flows for the American River at Fair Oaks (USGS gage #1144650)

Flow alteration by dams often leads to downstream changes in channel morphology. As a result of reduced peak flows, width of the high-flow channel tends to decrease and the area of regularly inundated floodplain is reduced (Graf 2006). With the loss of flows that scour the streambed, vegetation can establish in the active channel, resulting in the loss of channel complexity and instream habitat structure (Magdaleno and Fernández 2011). Dams also impact sediment transport processes. Large dams completely block bedload transport and reduce suspended sediment transport by inducing deposition in the low-velocity waters of reservoirs. Since the construction of major dams in the Sacramento–San Joaquin basin, annual bedload transport has fallen by an average of 45%, with total bedload of particles greater than 8 mm decreasing by 42% (Minear 2010). When reaches below dams are deprived of their sediment load, a condition known as “hungry water” can occur, whereby flows still have the energy to move sediment but have lost their supply, resulting in downstream erosion and bed incision (Kondolf 1997). Exceptions occur when flows have been reduced to the point that they can no longer carry sediments from downstream tributaries, resulting in aggradation (Kondolf et al. 2012).

4 | RESTORING FLOWS FOR FISH BELOW DAMS

Finally, an obvious, but perhaps underappreciated effect of dams is the creation of artificial reservoirs, which have considerably different physical and ecological properties than free-flowing rivers. The conversion of lotic (flowing water) to lentic (standing water) freshwater ecosystems alters the flux of nutrients and organic matter through river networks, increases surface water losses through evaporation, and creates novel habitats to which native biota may be poorly adapted. In regions that naturally have few perennial freshwater lakes, such as California’s coast ranges, the creation of artificial reservoirs by dams represents a significant transformation of river ecosystem structure and functions.

EFFECTS OF DAMS ON CALIFORNIA’S FISH POPULATIONS

California’s native freshwater fish species are experiencing widespread and rapid decline. A recent assessment of California’s freshwater fish populations indicates that 76% of the state’s native fish species are vulnerable to extinction if present trends continue (Moyle et al. 2011). Predicted effects of climate change are likely to accelerate this declining trend (Moyle et al. 2012). While many factors have contributed to the imperilment of California’s native fish species, the alteration of river ecosystems by dams is recognized to be a dominant driver of population declines (Moyle 2002; Katz et al. 2012; Moyle et al. 2011).

Dams have particularly impacted California’s anadromous fish populations, including commercially and culturally significant salmon and steelhead trout (Katz et al. 2012), but also several species of lamprey and sturgeon (Moyle 2002). Dams create barriers along river corridors that restrict or completely block access to upstream habitat of migratory species. For example, construction of impassable dams in the Sacramento River basin has reduced availability of habitat historically used by salmon and steelhead by more than 70% (Yoshiyama et al. 2001; Lindley et al. 2006). Migratory fish species also encounter many small dams, diversions, and culverts that obstruct movement; there are more than 6,200 documented barriers to fish passage and an additional 6,000 barriers with the potential

INTRODUCTION | 5 to block fish passage (CDFW 2012). The loss of habitat connectivity within river networks has significant implications for the persistence of anadromous fishes and other cold-water species, because warming water temperatures from climate change is expected to reduce the suitability of remaining accessible habitats below dams (Katz et al. 2012; Moyle et al. 2012).

The alteration of flows below dams is generally considered to be the most serious threat to ecological sustainability of rivers (Bunn and Arthington 2002; Nilsson et al. 2005; Dudgeon et al. 2006). Fish and other aquatic organisms are highly adapted to the natural seasonal flow variability that characterizes river ecosystems (Lytle and Poff 2004). For example, adult Pacific salmon typically enter California’s rivers to begin their migration to spawning grounds following the first major storms of the year, when elevated flows facilitate upstream passage (Moyle 2002). Spawning often occurs in the early spring, when flows are still elevated by the risk of egg mortality by bed- scouring flows is low (Montgomery et al. 1999). Out-migrating juvenile salmonids take advantage of seasonally inundated floodplains in the spring for rearing, which improves their growth and survival (Opperman et al. 2010). Other native species such as the Sacramento splittail (Pogonichthys macrolepidotus) are also dependent on the inundation of floodplain habitats in the early spring for spawning (Moyle 2002). Therefore, when seasonal patterns in the timing and magnitude of flows (including floodplain inundation flows) are altered by dams, many species are unable to successfully complete their life cycles.

Dams also cause downstream incision and reduction in channel complexity (Graf 2006), deteriorating the quality and availability of habitat for fish and other aquatic biota. The disruption of sediment transport can lead to the coarsening of channel bed materials and loss of spawning habitat for salmon, trout, and other species. In several of California’s regulated rivers, gravel is regularly imported and deposited below dams to maintain spawning habitat for threatened salmon populations (Pasternack et al. 2004).

6 | RESTORING FLOWS FOR FISH BELOW DAMS

Finally, dams impair native fishes by facilitating establishment of non-native species (Bunn and Arthington 2002). Reservoirs provide slow-water habitat favorable to non-native fishes such as common carp (Cyprinus carpio), (Micropterus salmoides), sunfishes (Lepomis spp.), and mosquito fishes (Gambusia spp.), which often outcompete or prey upon resident natives. The stabilization of river flows downstream of dams also promotes non-natives species, for example, by reducing the frequency and intensity of flood disturbance that would otherwise suppress their populations (Marchetti and Moyle 2001).

SECTION 5937 AND ‘FISH IN GOOD CONDITION’

The potential for dams to harm fish and fisheries has long been recognized in California. As early as 1852, less than two years after California entered the Union, the state Legislature outlawed the placement of instream obstructions to salmon migrations (Börk et al. 2012). Subsequent laws enacted in 1870 and 1880 further protected migratory fish. Nevertheless, repeated reports of drying rivers indicated that many dam operators ignored early fish passage laws (Börk et al. 2012). A 1914 Fish and Game Commission study that documented impacts of low water flows on fish prompted the Legislature to enact the 1915 Flow Act, which explicitly required flow releases below dams to protect fish. This law eventually became Section 5937 of the state Fish and Game Code, which states:

“The owner of any dam shall allow sufficient water at all times to pass through a fishway, or in the absence of a fishway, allow sufficient water to pass over, around, or through the dam, to keep in good condition any fish that may be planted or exist below the dam.”

The language plainly indicates that the dam owners have the responsibility to release enough water to support fish. But what does it mean to maintain “fish in good condition” and what flows below dams are required to do so?

INTRODUCTION | 7

“Good condition” is not explained in the code, but has been defined through a series of court decisions in the 1990s (Moyle et al. 1998). In essence, fish downstream of dams are considered to be in good condition when the species present are comprised of healthy individuals with self-sustaining populations and represent an assemblage that is dominated by native species and is persistent over time (Box 1). In the context of Section 5937, maintaining fish in good condition requires a flow regime that allows for downstream fish to complete their life history cycles, reproduce successfully in most years, and maintain a species assemblage that is resilient to disturbance.

Box 1

Table 1

Dr. Peter Moyle has provided an interpretation of “fish in good condition” that has been used in legal decisions concerning Section 5937 (Moyle et al. 1998). The condition of fish is assessed at the individual, population, and community level.”

Health at the individual level means that fish have a (1) robust body composition; (2) are relatively free of disease, parasites, and lesions; (3) should have reasonable growth rates for the region; and (4) respond in an appropriate manner to stimuli. This can be generally assessed by examining the condition and growth rates of individual fish. At the population level, good condition means that populations of individual species (1) contain multiple age classes (evidence of reproduction); (2) a viable population size; and (3) healthy individuals (as above).

At the community level, good condition is defined as a fish assemblage that is (1) dominated by native, co-evolved species; (2) has a predictable structure as indicated by niche overlap among the species and multiple trophics levels; (3) is resilient to recovering from extreme events; (4) is persistent in species membership through time; and (5) is replicated geographically.

8 | RESTORING FLOWS FOR FISH BELOW DAMS

APPLYING SECTION 5937 TO RESTORE FLOWS BELOW DAMS

Despite the clear language and intent of Section 5937 to protect fish below dams, dam owners have generally not met this requirement and the state agencies charged with its implementation have not enforced it (Börk et al. 2012). However, recent lawsuits have re-affirmed the need to provide adequate flows for fish under Section 5937 (Börk et al. 2012), and illustrate how the code could be applied to other river systems. offers a notable example of the successful application of Section 5937 in California (Box 2). However, Section 5937 has also played an important role in restoring flows to streams that drain into Mono Lake (California Trout, Inc. v. State Water Resources Control Board and California Trout, Inc. v. Superior Court) and in increasing water releases for fish below Friant Dam in the (NRDC v. Patterson).

While these cases provide useful illustrations of the application of Section 5937, specific flows requirements to maintain fish in good condition are highly context-dependent. For example, large regulated rivers that support salmon and other anadromous species below dams will have substantially different flow needs than streams in upper watersheds that support resident native species. Under Section 5937, all waterways below dams that would naturally have perennial flows should have sustained minimum flows needed to support a “living stream” (Moyle et al. 1998). However, the magnitude and timing of flow releases needed to support fish will require consideration of the natural flow regime and ecological requirements of the species present (or potentially present under restored conditions) within the river of interest.

INTRODUCTION | 9

Box 2

In the 1950s, the U.S. Bureau of Reclamation built Monticello Dam on Putah Creek, a tributary to the Sacramento River in Yolo County. Stream flow in lower Putah Creek is completely regulated, except when large storms cause the dam to spillover. During a late 1980s drought, releases were so meager that a 30-km section of lower Putah Creek dried, resulting in fish kills and harm to riparian wildlife. In response, a citizen’s group, UC Davis and the City of Davis sued to increase flows (Putah Creek Council v. Solano Irrigation District and Solano County Water Agency). The trial court, citing Section 5937, ordered a 50% increase in the minimum release schedule to keep the creek flowing to its mouth. Subsequent negotiations led to the Putah Creek Accord (Accord), signed in May 2000, which established additional operational requirements to benefit fish and other aquatic organisms (Moyle et al. 1998).

The Accord’s flow recommendations were based on the ecological needs of species and assemblages in the creek and were derived from the three-tiered definition of fish in good condition (Box 1, Moyle et al. 1998). The recommendations included increased spawning and rearing flows for native fish; pulse flows to attract and support anadromous fish; minimum flows to sustain fish in droughts.

Nine years of creek monitoring indicates that the new flow regime has been successful in promoting the expansion and health of native-dominated fish assemblages throughout the creek (Kiernan et al. 2012). Importantly, the restoration of native fishes was achieved by manipulating stream flows at biologically important times of the year and only required a small increase in the total volume of water delivered downstream (i.e., water that was not diverted most years).

The requirements of Section 5937 are also not static in time. In calling for downstream flows that keep fish in good condition “at all times”, the code allows for flow requirements to be adapted to changing circumstances in the future. This is particularly relevant with respect to climate change, which is expected to cause warmer water temperatures, altered flow patterns, and water quality degradation, all threats to California’s freshwater fish (Moyle et al. 2012). Therefore, the successful application of Section 5937 requires an adaptive approach, whereby flow requirements may be modified in response to changes in the local environment and fish community conditions, as determined by biological monitoring.

10 | RESTORING FLOWS FOR FISH BELOW DAMS

Sections 5937’s legal requirement to ensure adequate flows for fish potentially applies to thousands of dams in California. However, determining which dams may not be in compliance with the code is a daunting task that state agencies have not undertaken to date. The number of dams and unique biological, hydrological and geographic characteristics of each affected river suggest that a systematic approach is needed to identify dams where improved downstream flows may be required. Although site-specific studies will be necessary to ultimately determine the need for Section 5937 flows, an initial screening of dams based on indicators of hydrologic alteration and fish community condition, will help to prioritize sites for Section 5937 compliance.

A SYSTEMATIC APPROACH FOR EVALUATING DAMS

The primary goal of this study was to develop an approach to identify and evaluate California dams that have impaired downstream fish communities associated with altered flow regimes. The evaluation follows a systematic, six-step process that focuses on the inventory, characterization, and selection of dams where environmental flows may be warranted under Section 5937 (Figure 3). First, a database of dams is compiled and used to define their distribution and characteristics. Next, hydrologic conditions below dams are assessed to quantify the extent to which flows may deviate from natural, unimpaired conditions. Third, condition of native fish near each dam is evaluated. The fourth step is the identification of regulatory considerations that could affect implementation of environmental flows below specific dams. In the fifth step, dams with evidence of hydrologic alteration and indicators of fish community impairment are identified and ranked. For the sixth and final step, we select a subset of dams for initial assessment of their potential effects on native fish downstream. The assessments are a diverse series of case studies from different regions of California.

INTRODUCTION | 11

Figure 3 Conceptual diagram of dam evaluation approach

This investigation is a first attempt at developing a comprehensive, data-driven approach for evaluating California’s major dams and their impacts on native fish species in the context of Section 5937 requirements. The evaluation identifies dams where altered downstream flow regimes may be harming native fish. Deficiencies in the quality and resolution of data on dam operations and their effects on downstream fish make it impossible to conclusively assess Section 5937 compliance. The evaluation, nevertheless, provides clear indication of which dams are associated with evidence of biological and hydrological alteration and can be immediately used for setting priorities for further research, including site-specific studies on the effects of dam operations on fish.

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METHODS | 13

METHODS

STEP 1. BUILDING A DAM DATABASE

We developed a database of California dams from three datasets: the Army Corps of Engineers’ (USACE) National Inventory of Dams (USACE 2010), the Jurisdictional Dams from the California Department of Water Resources (DWR 2010), and the National Marine Fisheries Service’s (NMFS) Dam Dataset for Assessing Anadromous Fish Passage (Goslin 2005). The USACE and DWR datasets are comprised of dams at least 1.8-m (6-ft) high with a storage capacity greater than 60,000 m3 (50 acre feet), or that are more than 7.6-m (25-ft) high and store at least 18,500 m3 (15 acre feet).

The NMFS dataset was synthesized from earlier versions of the USACE and DWR datasets, but includes quality-controlled geographic location of dams in a GIS, based on the 1:100,000 National Hydrography Dataset (NHD) (Horizon Systems 2012). The NMFS dataset was used as the foundation of the database, which was updated with unique records and attributes from the more recent USACE and DWR datasets. New dam records added to the database were mapped in a GIS by their latitudinal and longitudinal coordinates, and, where necessary, manually relocated to the correct position based on the NHD streamline layer and ortho-rectified aerial photos.

We then filtered the database for dams with potential to be managed for environmental flows (Figure 4). First, we excluded dams not directly located on a stream channel, based on the NHD 1:100,000- scale streamlines. This included hydropower facilities (e.g., forebays) that do not drain directly into streams and projects located in urbanized catchments, such as wastewater treatment facilities, percolation basins, and urban ponds. Debris basins, retention ponds, and other passive impoundments were also excluded. For dams comprised of multiple project works (e.g., those with multiple dikes and spillways), we included only the primary impoundment structure. Finally, dams with drainage areas less than 1 km2 (0.4 mi2) and with storage capacities less than 100,000 m3 (80 acre feet) were excluded. While these dams are also subject to Section 5937, we considered them low-priority for this initial assessment based on their small size and location in upper watersheds.

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Figure 4 Evaluation approach and criteria for identifying dams where improved downstream flows may be warranted for Section 5937 compliance

METHODS | 15

STEP 2. ASSESSING FLOW REGIME ALTERATION BELOW DAMS

Dams have the potential to alter flow regimes in ways that significantly affect fish and other aquatic biota, including changes in the timing and magnitude of flows and disruption of natural patterns of seasonal flow variability (Bunn and Arthington 2002; Poff et al. 1997). To assess the degree of hydrologic alteration below dams in California, we examined USGS flow gaging records at, or near (within 1 km downstream) dams. The analysis included only gages with at least 10 years of daily flow records between 1970 and 2012.

We assessed potential changes in the magnitude and seasonality of monthly flows and changes in the magnitude of maximum 1-day flows below gaged dams (Figure 4). Predictions of expected, unimpaired monthly and maximum 1- day flows were generated using a statistical modeling approach developed by USGS (Carlisle et al. 2010a; Carlisle et al. 2010b). The models parameterize relationships between geospatial attributes (e.g., climate, topography, soils) and hydrologic responses at reference gages (i.e., those with no upstream dams and limited land use disturbance) to predict hydrologic conditions at dams based on upstream catchment characteristics. Deviation from expected flow magnitudes was assessed by the ratio of observed (calculated from daily flow records) to expected (modeled) values. Alteration to seasonal flow patterns was also assessed by quantifying the correlation between observed and expected mean monthly flows (Batalla et al. 2004; Kondolf and Batalla 2005). Pearson’s correlation coefficient (r) was calculated, which varies between -1 and 1, with a value of 1 indicating a positive (increasing) correlation and -1 indicating a negative correlation. Deviation from expected seasonal flow patterns is expressed as decreasing values from 1.

Because of the limited distribution of USGS gage stations, information on downstream flows was not available for the majority of dams evaluated in this study. However, the potential for flow alteration was assessed for all dams by the impounded runoff (IR) ratio, which is the reservoir storage capacity divided by the mean annual inflow. The IR reflects the

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dam’s capacity to capture a river’s flow and is strongly correlated with indicators of hydrologic alteration, such as reductions in peak-flow magnitudes and disruption of seasonal flow patterns (Batalla et al. 2004; Kondolf and Batalla 2005; Singer 2007). Mean annual inflow at each dam was calculated by the statistical modeling approach (described above). The storage capacity for each dam was derived from values reported in public dam datasets (USACE 2010; DWR 2010). The cumulative impounded runoff (CIR) was also calculated to consider the potential influence of dams from the upper catchments on a downstream dam. For each dam, the reservoir storage capacity was added to the storage capacity of all reservoirs in the upstream catchment area, which was then divided by the mean annual inflow.

STEP 3. ASSESSING CONDITION OF NATIVE FISH BELOW DAMS

To assess condition of fish in rivers affected by dams, we used PISCES (Viers et al. 2012), a GIS database and visualization system for mapping, modeling and analysis of California native fish species. PISCES incorporates empirical data and expert knowledge to estimate historic and current species’ ranges at the Hydrologic Unit Code 12 (HUC12) watershed scale. Within California, there are 4,644 HUC12 watersheds, which have an average area of 91±54 km2 [35±20 mi2 (mean±SD)]. Because of the spatial scale at which data are compiled in PISCES, data on fish assemblages are generally not distinguished for river reaches above and below dams within a HUC12 watershed. Therefore, the indicators of fish community condition are associated spatially with dams, but do not necessarily reflect the causal effects of dam operations on fish.

“Fish in good condition” at the community level is defined by an assemblage of species that is persistent in time (Box 1). Therefore, the loss of native species from HUC12-watersheds affected by dams was selected as a potential indicator that the fish community is not in good condition. To determine if native fish species have been lost in watersheds affected by dams, we compared historic to current range maps and calculated the change in native species richness for all watersheds. The

METHODS | 17 analysis focused on 28 native species for which reliable historic and current range information was available. All dams were identified that have lost native species from the HUC12 watershed within which they occur.

Fish in good condition also applies at the population level. To assess the condition of native fish populations potentially affected by dams, current species range maps were integrated with a recent assessment of population status (Moyle et al. 2011). As part of the assessment, each of California’s 129 native fish species was assigned a conservation status, indicating whether their population is extinct (0), endangered (1), vulnerable (2), near-threatened (3), or relatively secure (4). For this study, we considered all species with a status of 2 or less to be an indicator that a population may not be in good condition. We identified all dams within the current range of these “sensitive species” (n = 66, Appendix A), which could potentially be affected by the operation of upstream dams.

As a final criterion, we identified dams within the current range of Pacific salmon listed as threatened and endangered under the federal Endangered Species Act (ESA). These species include Central Valley spring- and winter-run and California coast Chinook salmon (Oncorhynchus tshawytscha), Central California coast and Southern Oregon/Northern California coho salmon (O. kitsutch), and several distinct population segments of steelhead trout (O. mykiss), including Southern California, Central and South Central California coast, Central Valley, and Northern California. These populations are all considered “sensitive” (as defined by the Moyle et al. (2011) population status of 2 or less) and are evaluated independently because of their high conservation importance, fishery value, and cultural significance.

Once the set of criteria describing hydrologic- and fish conditions was compiled for each dam, we explored the association among variables. A robust statistical analysis of the relationships between dam-related flow alteration and fish condition was beyond the scope of this study. However, a series of box plots were generated to provide an initial qualitative assessment of the associations among the hydrologic and ecological variables.

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STEP 4. IDENTIFYING REGULATORY CONSIDERATIONS

The fourth step in dam evaluation involves identification of regulatory considerations relevant to Section 5937. Because the goal of this study is to identify dams that may require improved downstream flows to support native fish, those with established regulatory processes to protect environmental flows were filtered from the analysis. For example, hydropower dams regulated by the Federal Energy Regulatory Commission (FERC) are subject to a licensing process that requires environmental flows to mitigate impacts to downstream biota. Therefore, implementation of Section 5937 at FERC dams is considered a lower priority than at dams not subject to FERC regulations. For this reason, we excluded all FERC-regulated dams for evaluation. Likewise, we excluded dams subject to a federal biological opinion requiring environmental flows for ESA-listed species.

STEP 5. IDENTIFYING AND RANKING CANDIDATE DAMS

The goal of this step in the evaluation process is to identify a subset of candidate dams for which evidence of hydrologic alteration and fish community impairment exists, excluding those subject to federal environmental flow requirements.

The criteria for hydrologic alteration were based on deviation from observed flow patterns (magnitude of monthly and maximum 1-day flows and seasonality) and high values for impounded runoff and cumulative impounded runoff, which indicates that the dam has the potential to capture most or all of the rivers annual inflow at that location. There are no general, transferable quantitative relationships between flow alteration and ecological responses that can be used to set objective thresholds of flow impairment likely to harm fish and other stream biota (Poff and Zimmerman 2010). However, a review of environmental flow standards suggested that flow alteration greater than 20% is likely to cause moderate to major changes in natural ecosystem structure and functions.

METHODS | 19

(Richter et al. 2011). There is also evidence that the risk of ecological impairment consistently increases with the magnitude of hydrologic alteration (Carlisle et al. 2010b; Poff and Zimmerman 2010).

We considered deviation in monthly and maximum 1-day flows of 50% as a reasonable threshold criterion, which is likely to result in ecological impacts and is large enough to limit the potential effects of model uncertainty on flow alteration (i.e., observed/expected flow metrics). The threshold criterion for deviation in seasonal flow patterns was defined by a Pearson’s r correlation coefficient of less than 0.5. Values greater than 0.5 indicate that observed and expected monthly flows are highly correlated, signifying that observed flow seasonality generally follows expected patterns. Finally, an impounded runoff (IR) or cumulative runoff (CIR) index greater than 0.75 was used as a criterion for hydrologic alteration, based on previous studies that have shown IR values to be a strong indicator of flow regime impacts (Kondolf and Batalla 2005; Singer 2007; Eng et al. 2012).

The criteria for selecting dams associated with fish community impairment included (1) the loss of at least one native fish species, (2) the presence of species with populations in decline or at risk of extinction, and (3) the presence of ESA-listed Pacific salmon. Using the PISCES database, we evaluated indicators of fish impairment at all HUC12 watersheds containing dams. Dams within watersheds that have lost at least one species (based on the comparison of historic versus current ranges of 28 native fish) were selected, as were dams in watersheds within the current range of sensitive species [i.e., conservation status of 2 or less per Moyle et al. (2011)]. Dams associated with ESA-listed Pacific salmon were also identified.

The final subset of dams consisted of those satisfying one or more of the hydrologic criteria and those associated with at least one indicator of fish impairment. These dams were then sorted and ranked by dam size (reservoir capacity), impounded (and cumulative impounded) runoff ratio, and other hydrologic impact criteria. These sorting criteria emphasize the largest dams and those with potential for significant hydrologic impacts. Additional sorting criteria were applied to highlight dams affecting fish assemblages of potential conservation

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significance, and included the number of sensitive species and total number of native species potentially present in the affected watershed.

STEP 6. PRELIMINARY CASE STUDY INVESTIGATIONS

Several case study dams were selected from the final subset (Step 5). These dams are not necessarily those most in need of environmental flow management. Rather, they exemplify the broad geographic distribution of dams in the state and illustrate the diversity of dam types, size and operations. For each dam, we describe its basic structural and operational characteristics, current downstream flow regime, and the native fish species potentially affected. Where available, technical reports and other relevant sources were used to validate and expand upon results of the evaluation.

EVALUATION RESULTS | 21

EVALUATION RESULTS

A total of 1,440 unique California dam records were compiled from existing datasets (Goslin 2005; USACE 2010; DWR 2010). From this list, 515 were identified as off-stream dams, retention basins, or other facilities that do not release water directly into streams. An additional 172 dams with small drainage areas [<1 km2 (<0.4 mi2)] and/or low storage capacities [<100,000 m3 (<80 acre feet)] were excluded. The 753 remaining dams were selected for further assessment (Appendix B). These dams represent a broad range of sizes, storage capacities, and drainage areas (Figure 5). The dams also include those that are privately owned (n = 339) and those owned and operated by local (n = 279), state (n = 27) and federal agencies (n = 108).

Figure 5 Dams evaluated in California (n =753) with frequency distributions of dam height, storage capacity, and upstream catchment areas

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FLOW REGIME ALTERATION BELOW DAMS

A total of 209 USGS flow gages were identified at or immediately downstream of dams. Potential alteration to flow magnitudes and seasonal flow patterns was first assessed by comparing modeled mean monthly flows (representing expected hydrologic conditions in the absence of dams) with observed flows. Only gages with at least 27 days of daily flow records per month for 10 years or more were included, resulting in 172 gages below 185 dams. For most gage sites, the ratio of observed-to-expected (O/E) mean monthly flows was less than 1, indicating that flow releases from dams are, on average, lower than expected. Monthly O/E values were generally lower in winter and spring (Nov-May) than in the summer and fall (Jul-Oct) when values were greater than 1 for some sites (Figure 6). This probably represents the effects of water storage and in the winter, and augmented flow releases in the late summer for agricultural water deliveries. Comparisons of observed and predicted flows at reference gages indicated that the model was unbiased and reasonably accurate (Appendix C).

All gaged dams had evidence of some degree of monthly flow alteration. Among the 185 dams evaluated, each one had at least one month in which observed monthly flows deviated from expected values by more than 50%. For 66 dams, monthly flows were altered by more than 50% for all 12 months, and for the vast majority of dams (n = 171), monthly flows were altered by 50% for 6 or more months.

EVALUATION RESULTS | 23

Figure 6 Histograms of observed/expected mean monthly flows for all gaged dams. O/E values between 0.75-1.25 (gray bars) indicate that observed flows are similar to expected values

24 | RESTORING FLOWS FOR FISH BELOW DAMS

Next, potential effects of dams on downstream peak flows were assessed by comparing observed with expected values of mean maximum 1-day flow. Only gages with more than 350 days of daily flow records per year for 10 years were included, resulting in 153 unique sites. Maximum 1-day flows were generally lower than expected values, indicating a reduction in peak-flow magnitudes below most dams (Figure 7). Of 153 sites evaluated, observed maximum 1-day flows were less than 50% of expected values at more than half (n = 83) of the gages.

Figure 7 Histogram of observed/expected maximum 1-day discharge. O/E values near 1 (gray bar) indicate that observed flows are similar to expected values

Changes in seasonal flow patterns were assessed by examining the correlation between observed and expected monthly flows. For the majority of gages (n = 125 of 172), observed and expected monthly flows were strongly correlated (r > 0.75), indicating that monthly seasonal flow patterns were largely preserved. However, low correlation (r < 0.5) of monthly flows below several dams provides evidence that seasonal flow patterns have been highly altered in some rivers (Figure 8). There were 14 gages with correlation values less 0, indicating a reversal of natural seasonal flow patterns in those affected

EVALUATION RESULTS | 25 rivers. An example of a dam in which downstream flows closely follow expected seasonal patterns is the R.W. Mathews Dam on the Mad River (r = 0.99, Figure 9). Deviation from expected seasonal flow patterns is evident below dams such as New Melones Dam on the Stanislaus River (r = 0.63) and Indian Valley Dam on North Fork Cache Creek (r = 0.05)

Figure 8 Histogram of correlation coefficient between observed and expected monthly flows, for all gages below dams. Gray bar denotes high correlation, or strong correspondence, between observed and expected seasonal monthly flow patterns

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Figure 9 Examples of seasonal flow alteration below dams, as measured by correlation between expected (modeled unimpaired) and observed mean monthly flows

EVALUATION RESULTS | 27

The impounded runoff (IR) values exhibited a bi-modal distribution, with most dams having either values less than 0.2 (i.e., storage capacity less than 20% of annual inflow volume) or greater than 1 (i.e., storage capacity greater than mean annual inflow) (Figure 10). A total of 345 dams have an IR greater than 0.5, 229 greater than 0.75, and 178 greater than 1. Storage capacity is thus strongly correlated with expected annual discharge, suggesting that many dams in California are designed to capture a significant proportion of available annual supplies. Thus, even dams that are relatively small may capture most or all of the annual discharge of an affected river or stream. While dams with high IR-values occur throughout the state, they are clustered in particularly high densities in arid regions, such as southern coastal California and the Modoc plateau (Figure 10).

Figure 10 Impounded runoff (IR) ratio for dams in California, representing the capacity relative to the (modeled) mean annual inflow; inset map illustrates the difference between IR and CIR for series of dams on the Pit River

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The cumulative impounded runoff (CIR) ratio reflects the potential effects of all dams in the catchment above a specific dam of interest. For example, the series of dams on the Pit River have individually low IR values (<0.1), but because they are below Lake Almanor, a large reservoir with a high IR value (>1), downstream flows are likely to exhibit greater impairment than otherwise expected (inset map in Figure 10).

To evaluate how the IR and CIR relate to observed patterns of hydrologic alteration at gaged dams, the O/E and seasonality metrics were plotted against IR and CIR (only CIR presented, Figure 11). There was substantial variability in the data, but average monthly O/E values were positively correlated with CIR, signifying that higher CIR values are associated with increased deviation in monthly flows. In contrast, there was a weak negative relationship between O/E maximum 1-day values and CIR, indicating that dams with greater CIR values tend to reduce peak flows. Pearson’s r, signifying the correlation between observed and expected seasonal flow patterns, was not highly correlated with CIR. However, low values of Pearson’s r occurred more frequently at high CIR values (>0.5) than at low CIR values, indicating that degree of seasonal flow alteration may be higher for dams with high CIR.

EVALUATION RESULTS | 29

Figure 11 Relationship between O/E monthly flows, O/E maximum 1-day flows, Pearson’s r and the cumulative impounded runoff (CIR) ratio at gaged dams

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INDICATORS OF FISH CONDITION

To assess the condition of fish in river basins affected by dams, we first evaluated the association of dams with the loss of native species from their historic range. Based on the 28 fish taxa for which reliable historical distribution data exists, at least one species has been lost from 265 (HUC12) watersheds affected by 263 dams (Figure 12). Dams associated with the loss of species were concentrated in the central and southern California coast, the Sierra Nevada foothills and in the upper Sacramento and Klamath river basins. Among species with known historic ranges, Arroyo chub, Central Coast coho salmon, Central Valley fall Chinook salmon, and Sacramento perch were the most common species to be lost from watersheds affected by dams.

Figure 12 Patterns of species loss from HUC12 watersheds for 28 native fish species with historical and current range data

EVALUATION RESULTS | 31

The condition of native fish populations was then evaluated by integrating range maps with the Moyle et al. (2011) population status assessment, yielding a statewide map of sensitive taxa richness at the HUC12-watershed scale (Figure 13). All dams falling within range of sensitive species populations (considered endangered or vulnerable) were then identified. The regions of California supporting the highest richness of sensitive species populations are the Central Valley, the Sacramento-San Joaquin River Delta, the upper Sacramento River, and Klamath River Basin (Figure 13).

Figure 13 Patterns of sensitive species richness within California’s HUC12 watersheds; population status of each native species based on Moyle et al. 2011

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A total of 378 dams are within the range of at least 1 sensitive species. Of these, 211 are within the range of anadromous ESA- listed salmon and steelhead trout species, such as the endangered Southern California steelhead trout (Figure 14).

Figure 14 Current distribution of anadromous salmonid species, listed as threatened or endangered under the federal Endangered Species Act

EVALUATION RESULTS | 33

RELATIONSHIPS BETWEEN HYDROLOGIC ALTERATION AND FISH CONDITION

A series of box plots were generated to explore relationships between hydrologic variables and fish community characteristics. First, the total richness of native fish species was compared with hydrologic metrics for each dam. There was a positive association between the number of native species present and estimated annual discharge and cumulative storage. This indicated that species richness tends to increase with river size (Figure 15). However, there was no apparent trend between native species richness and other indicators of hydrologic alteration.

Figure 15 Native species richness plotted against annual discharge and cumulative storage

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Next we examined the association between the number of sensitive species present (plus any native species extirpations) and the hydrologic alteration metrics. There was substantial variation in the data for all variables, but differences among the species richness bins were generally small. The total number of sensitive and lost species was slightly greater for dams with large mean annual discharge and cumulative storage (Figure 16). In addition, dams with no sensitive species had the lowest mean value for impounded runoff, cumulative impounded runoff, and maximum 1-day flow deviation (Figure 17). Differences in sensitive species richness did not appear to vary significantly by the degree of monthly and seasonal flow deviation.

Figure 16 Number of sensitive species plus species losses, plotted against annual discharge and cumulative storage capacity

EVALUATION RESULTS | 35

Figure 17 Number of sensitive species plus species losses, plotted against impounded runoff (IR), cumulative impounded runoff, monthly flow deviation, maximum 1-day flow deviation, and seasonal flow deviation; flow deviation metrics are transformed: increasing values (from 0) indicate increasing degree of deviation from modeled unimpaired conditions

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DAMS SUBJECT TO FEDERAL ENVIRONMENTAL FLOW REQUIREMENTS

A total of 165 dams were excluded because they are subject to federally determined environmental flows (Figure 18). These included 159 FERC-regulated dams and others, such as that operate under a federal biological opinion to protect ESA-listed species.

Figure 18 Dams with (gray, n = 165) and without (black, n = 588) known federal environmental flow requirements

EVALUATION RESULTS | 37

IDENTIFICATION AND RANKING OF CANDIDATE DAMS

Of the 753 dams evaluated, 385 were associated with at least one indicator of altered downstream flows. All 185 gaged dams had modified monthly flows (deviation greater than 50%) in at least one month, while 91 of them were associated with impaired maximum 1-day flows (deviation greater than 50%), and 41 had evidence of significant seasonal flow alteration (i.e., weak correlation between observed and expected monthly flow patterns). A total of 288 dams had IR or CIR values greater than 0.75.

Among all 753 dams, 495 were associated with at least one indicator that fish are not in good condition (e.g., loss of species or presence of sensitive species populations). For 263 dams, at least one species has been lost its HUC12 watershed, while a total of 378 dams are within the range of sensitive species. A total of 268 dams (of the 495 with indicators of fish impairment) also had evidence of flow regime alteration. Excluding dams with federally regulated environmental flows, there are 220 remaining candidate dams considered high priority for assessing compliance with Section 5937 (Appendix D, Figure 19).

Figure 19 High priority candidate dams (n = 220) for assessing compliance with Section 5937

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To further examine the final subset, candidate dams were ranked and sorted by their physical features (reservoir capacity), hydrologic indicators (degree of seasonal flow alteration), and associated fish community characteristics. Dams with large storage capacities are ranked because of their influence on downstream water availability for fish is likely significant. Also, most large storage dams are designed to control the timing and magnitude of flow releases, which could facilitate the conjunctive management of reservoirs for multiple benefits, including flows for fish. Dams with the largest water storage capacities include Trinity Dam on the Trinity River, New Melones Dam on the Stanislaus River, Pine Flat on Kings River, and on the American River (Table 1). Dams associated with the greatest downstream hydrologic alteration were also identified and ranked by correlation of observed to expected mean monthly flows. Among the subset of dams with downstream USGS gaging stations (n = 185), Tinemaha Dam on the Owens River, Anderson Dam on Coyote Creek, and Calaveras Dam on Calaveras Creek were associated with the greatest alteration to seasonal monthly flow patterns (Table 1).

EVALUATION RESULTS | 39

Table 1 Top 20-ranking dams sorted by storage capacity and seasonal flow deviation

Rank Storage capacity (106 m3) Monthly flow deviation (r)a

1 Trinity 3,019 Tinemaha -0.55 2 New Melones 2,960 Anderson -0.03 3 Pine Flat 1,233 Calaveras -0.01 Mendota 4 Folsom 1,203 0.11 Diversion 5 Warm Springs 470 Crocker Diversion 0.12 6 San Antonio 432 San Antonio 0.16 7 Nacimiento 419 Bradbury 0.23 8 Castaic 399 Nacimiento 0.27 9 New Hogan 391 Seven Oaks 0.32 10 Casitas 313 Keswick 0.37 11 Twitchell 296 Lewiston 0.45 12 Stampede 279 0.55 13 Bradbury 253 West Valley 0.57 14 Long Valley 226 Success 0.61 15 Mathews 224 New Melones 0.62 16 Seven Oaks 180 Casitas 0.63 17 Black Butte 177 Donner Lake 0.65 18 Lake Kaweah 176 Lake O’Neill 0.70 19 Coyote Valley 151 Dwinnell Dam 0.74 20 El Capitan 139 Martis Creek 0.74 a. Assessed only at dams with downstream gages (n = 185) by calculating the correlation between observed and expected (modeled) mean monthly flows.

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Candidate dams associated with a high richness of native species and sensitive species were also identified. The highest- ranking dams are those in watersheds that support particularly high fish biodiversity. This suggests that their management would be important to native fish conservation. Dams associated with the greatest richness of native species include Woodbridge Diversion Dam on the Mokelumne River, Nash Dam on a tributary to Stillwater Creek in Shasta County, and a series of three Rubber Dams on lower (Table 2). The dams associated with the greatest number of sensitive species included Keswick and Anderson-Cottonwood dams on the Sacramento River, Woodbridge Diversion Dam, and Nash Dam (Table 2).

EVALUATION RESULTS | 41

Table 2 Top 20-ranking dams sorted by native species richness and sensitive species richness

Rank Native species richness Sensitive species richness

1 Woodbridge Diversion 10 Keswick 6 2 Nash 10 Woodbridge Diversion 6 3 Alameda Creek Rubber Dams 9 Anderson Cottonwood 6 4 Folsom 9 Nash 6 5 Nimbus 9 Folsom 5 6 Goodwin 8 San Pablo 5 7 Crocker Diversion 8 Nimbus 5 8 Farmington 8 5 9 New San Leandro 8 Crocker Diversion 5 10 Woodward 7 Lake Anza 5 11 Prosser Creek 7 Englebright 4 12 Lewiston 7 Lower Crystal Springs 4 13 Chabot 7 Farmington 4 14 Clementia 7 New San Leandro 4 15 Putah Diversion 7 Woodward 4 16 La Grange 7 Modesto Reservoir 4 17 (Don Castro) 7 San Andreas 4 18 Rodden Lake 7 Lewiston 4 19 Hamel 7 Chabot 4 20 Dry Creek 7 Guadalupe 4

Dams were also identified within the range of ESA-listed salmon and steelhead trout species (Table 3). The list does not include all dams within the species ranges – just those in the final subset of candidate dams. Only four candidate dams are within the range of Southern Oregon/Northern California coho salmon (ESA endangered): Trinity and Lewiston Dams on the Trinity River, Dwinnell Dam on the Shasta River, and Scout Lake Dam on a tributary to Berry Creek in Mendocino County.

Dams located within the range of ESA-endangered Central California Coast coho salmon are: Warm Springs Dam on Dry Creek in Sonoma County, Peters, Bon Tempe and Alpine Dams in the Lagunitas Creek watershed, Soulajule Dam on Arroyo Sausal (also in Marin County), and Newell Dam on the San Lorenzo River in Santa Cruz County.

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These dams are also within the range of ESA-threatened Central California Coast Steelhead Trout, as are San Antonio Dam on the San Antonio River in Monterey County, Nacimiento Dam on the Nacimiento River in San Luis Obispo County, and Coyote Valley Dam on the east fork of the Russian River in Mendocino County.

The largest dams potentially affecting Southern California steelhead trout (ESA endangered) are Casitas, Twitchell, and Bradbury Dams – on Coyote Creek, Cuyama River, and Santa Ynez River, respectively. There are 20 candidate dams within the range Central Valley steelhead trout (ESA threatened). The largest are Folsom, New Hogan, Black Butte, and Englebright.

EVALUATION RESULTS | 43

Table 3 Top 20-ranking dams sorted by ESA-listed salmon and steelhead trout populations

Southern Central Central Southern Central Valley Oregon/Northern California Coast California Coast California Steelhead Trout California Coho Coho Salmon Steelhead Trouta Steelhead Trout Trinity Warm Springs Warm Springs Casitas Folsom

Dwinnell Dam Peters San Antonio Twitchell New Hogan Dam

Lewiston Soulajule Nacimiento Bradbury Black Butte

Scout Lake Alpine Coyote Valley El Capitan Englebright Modesto Newell Calaveras San Vicente Reservoir Whittier Bon Tempe Anderson Keswick Narrows Lower Crystal Bean Hollow #2 Morena Nimbus Springs Lopez Barrett Anthony House Woodbridge James H Turner San Gabriel Diversion San Pablo Lake Hodges Davis No 2 New San Anderson Bouquet Canyon Leandro Cottonwood Whale Rock Santa Fe Clementia

Peters Morris Putah Diversion

Conn Creek Ramona Goodwin

Salinas Wood Ranch La Grange

San Andreas Gibraltar Nash

Hernandez Juncal Rodden Lake

Lake Curry Trampas Canyon Hamel Crocker Soulajule Mission Viejo Diversion Chabot Upper Oso Foothill Ranch a Top 20 largest (by storage capacity) of 48 candidate dams that occur within the range of Central California Coast steelhead trout.

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In summary, 220 dams were identified as sites where improved environmental flows are likely warranted under Section 5937, based on evidence of hydrologic alteration and indicators of fish population impairment. These dams are statewide (Figure 19) and represent a broad diversity of ownership (e.g., public utilities, private, state agencies), impoundment sizes and functions (e.g., flood control, water storage, and diversions). None is regulated by FERC, although some are subject to environmental flow requirements of federal or state agencies. Regardless, it is unknown whether flow releases from any of the candidate dams are managed to keep fish in good condition. While this analysis provides evidence of flow regime alteration and fish population impairment for all candidate dams, determination of Section 5937 compliance will likely require site-specific assessment.

PRELIMINARY SITE INVESTIGATIONS

We present 10 of the candidate dams as case studies to how operations may affect fish downstream (Table 4, Figure 20). The case-study dams are not necessarily those most in need of improved flows for fish. Rather, they serve to highlight the broad diversity of dams in California, in terms of their size, location, ownership, and function. Many of the case dams were selected from the ranked lists (Tables 1-3). In Chapter V, we describe for each of the 10 dams basic structural and operational characteristics, the downstream flow regime, and native fish species potentially affected.

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Table 4 Case study dams

Sensitive species Capacity Primary Dam County River Ownership potentially (106 m3) Purpose affected Central Valley Flood control Black Butte Army Corps steelhead, Central Tehama Stony Creek 177.3 and Dam of Engineers Valley fall-run and irrigation spring-run Chinook

Conn Creek Urban water Central California Napa Conn Creek 38.2 City of Napa Dam supply coast steelhead trout

Marin Central California Lagunitas Municipal Urban water coast coho salmon, Peters Dam Marin 40.5 Creek Water supply Central California District coast steelhead Central Valley steelhead, Central Recreation, Woodbridge Woodbridge Valley fall-run San Mokelumne 3.0 irrigation Diversion Irrigation Chinook salmon, Joaquin River and urban Dam District southern water supply sturgeon, white sturgeon Southern California Twitchell San Luis Cuyama Bureau of 296 Irrigation coast steelhead Dam Obispo River Reclamation trout, Arroyo chub Hydroelectric Owens tui chub, City of Los Long Valley Mono Owens River 226.3 and water Owens speckled Angeles supply dace, Owens pupfish Irrigation Southern California Bureau of Casitas Dam Ventura Coyote Creek 313.3 and water coast steelhead, Reclamation supply Arroyo chub Shortnose sucker, Lost River sucker, Boles Forest Modoc Boles Creek 6.2 Irrigation Klamath largescale Meadow Dam Service sucker, Klamath marbled sculpin Pine Flat Army Corps Fresno Kings River 1,233.5 Flood control Kern brook lamprey Dam of Engineers Southern Oregon/Northern Montague California coho Dwinnell Water Siskiyou Shasta River 61.6 Irrigation salmon, Upper Dam Conservation Klamath-Trinity District fall- and spring-run Chinook salmon

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Figure 20 Ten case study dams from the list of candidate dams (n = 220), selected to provide preliminary site investigation of the potential effects of dam operations on downstream fish

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DISCUSSION

SYSTEMATIC EVALUATION OF DAMS

This study offers a systematic framework for identifying dams that likely need improved downstream fish flows as required under Section 5937. From an original pool of more than 1,400 dams, we identified 220 as high-priority candidates for further investigation of environmental flow needs for fish. These dams fall within a broad range of biogeographic settings and represent a wide diversity in size, function and ownership.

For the vast majority of dams, flows observed at downstream gages deviated from expected natural patterns by at least 50% for at least six months of the year. In addition, for more than half of the gaged dams evaluated, maximum 1-day flows were less than 50% of predicted values. While model prediction error of expected flows could be contributing to apparent deviation from observed values, the lack of model bias (Appendix C) and magnitude of effects among gaged dams suggests that the deviation reflects true impacts of dam operations. Although several dams appear to have substantially altered seasonal flow patterns, flow seasonality has been largely preserved below the majority of gaged dams. This may be the result of water spilling over dams in winter and minimum flow releases in the summer, likely to provide water for downstream water rights holders.

The lack of gaging records restricted the hydrologic impact analysis to a relatively small subset of dams (about 200). However, the correlation between O/E- and seasonal flow alteration metrics indicates that the impounded runoff ratio is a reasonable proxy for predicting potential hydrologic alteration below dams. Thus, large IR values for many dams in the state suggest that alteration to downstream flows is likely.

A significant proportion of the dams assessed are within the range of least one native fish species considered at risk of extinction. A total of 378 dams (of the 753 assessed) are within the range of at least one sensitive fish species, including 211 within the range of ESA-listed anadromous salmonids.

DISCUSSION | 49

Furthermore, at least one native fish species has been lost from watersheds affected by 263 of the 753 dams.

There is some evidence that the number of sensitive species and species losses is associated with hydrologic alteration below dams. For example, dams with no sensitive species or extirpations tended to have lower deviation values in maximum 1-day flows and lower impounded and cumulative impounded runoff than dams with 1 or more sensitive species and extirpations. While the association of dams with sensitive fish populations or reduced species ranges is not causal evidence, the potential for dams to impair fish populations is well-established in California (e.g., Marchetti and Moyle 2001; Brown and Ford 2002; Brown & Bauer 2010; Moyle et al. 2011) and elsewhere (e.g., Gehrke and Harris 2001; Clavero et al. 2004; Rinne et al. 2005). Thus, it is reasonable to expect that dam operations are an important influence on the condition and persistence of fish populations.

LIMITATIONS

The investigation revealed a notably lack of information detailing dam operations, downstream flow regimes, and affected fish communities. The void presented a major challenge in building a standardized, high-resolution database of California dams and associated conditions. The National Inventory of Dams (USACE 2012) and State Jurisdictional Dam Database (DWR 2010) provided dimensions, location, and ownership of dams, but none of the operational information needed to effects on downstream flows. The vast majority of dams have no flow monitoring downstream. In those cases, we used the impounded runoff index as a proxy for hydrologic alteration.

The effects of California’s dams on downstream flows remains poorly documented. The study not only highlights the need for improved stream flow monitoring, but also for public reporting of dam operations and water use. To quantify potential hydrologic effects of diversion dams (which generally have a small storage capacity, but may divert substantial volumes of water), we examined the Water Rights Database of the State Water Resources Control Board (SWRCB 2012). This database includes coordinate locations for all points of diversion linked

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to the project’s water rights permit or license. But the database was not useful for quantifying the hydrologic effects of diversions because there was little concurrence between the face value of water rights and actual water use (e.g. assessed at flow gage or from secondary data source). The lack of accurate reporting of water use represents a significant impediment to managing for environmental flows in California’s rivers.

The UC Davis PISCES database (Viers et al. 2012) is the most comprehensive compilation of standardized data on California’s native fish species. PISCES is a software and data storage platform that uses primary source data, modeling, and expert analysis to generate best-known ranges for the state’s fish. But data are compiled and presented at the HUC12 watershed scale, making it impossible to distinguish between fish assemblages below and above dams. Thus, the spatial association of fish species with specific dams (upon which the selection criteria are based) is not definitive; indicators of fish community impairment (e.g. sensitive species or loss of species from historic range) below dams should be confirmed as part of site-specific investigations.

RECOMMENDATIONS

Our evaluation approach can be improved as new data and modeling tools become available. Additional monitoring data on downstream flows and fish communities could change the relative rankings of dams on the high-priority list. New criteria could also be incorporated in the evaluation framework to support the selection and ranking of high-priority dams for further assessment. For example, criteria based on the quality and quantity of downstream available fish habitat would help prioritize dams for environmental flow management. There is a broad suite of additional indicators of hydrologic alteration that could also be assessed below gaged dams (Olden and Poff 2003).

Also, information on the relative vulnerability of California’s fish assemblages to climate change is needed for informing environmental flow implementation strategies. Most dammed rivers in California support native fish species considered highly vulnerable to climate change (Moyle et al. 2012). For example, the availability of suitable habitat for many cold- water species such as salmon is likely to decrease in the future

DISCUSSION | 51

(Katz et al. 2012; Null et al. 2013). Modification of flow releases from dams to maintain cold-water habitat could be an important tool to reduce impacts of climate change on fishes.

The integrated database developed for this study can be used to examine the relationships between physical drivers of river alteration and ecological responses. In this study, associations between hydrological metrics and indicators of fish condition were examined through qualitative, exploratory analysis. While not conclusive or exhaustive, these relationships are strong indicators of the linkage between dam-driven flow changes and fish condition, and highlight the need for more robust, statistical analyses to quantify the effects of dam operations on California’s native fish assemblages. Such analyses could be helpful in developing environmental flow recommendations for regulated rivers throughout the state and elsewhere.

In summary, there is evidence that flows below many of California’s dams may be insufficient to maintain fish in good condition. Given the rapid decline of California’s fish fauna and pervasive alteration to the state’s river ecosystems, environmental flows are important if not critical to conservation of many native fish populations. Section 5937 requires that such flows be restored and protected. Other states and countries have similar legal mechanisms for protecting environmental flows (Annear et al. 2004; Arthington 2012; Gillilan and Brown 1997), including the Public Trust Doctrine (Frank 2012), of which 5937 could be regarded as an extension (Börk et al. 2012). Thus, our evaluation method is applicable beyond California where systematic assessments of dams could help guide the management and conservation of freshwater ecosystems.

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CASE STUDIES

Ten case study dams were selected from the 220 candidate dams associated with evidence of flow alteration and fish population impairment. Several dams were selected for their potential impacts to ESA-listed salmon and steelhead trout: Black Butte Dam on Stony Creek was selected because of its location in the upper Sacramento River basin and potential effects on Central Valley fall- and spring-run Chinook salmon and Central Valley steelhead trout. Conn Creek Dam is a smaller dam in the watershed managed for municipal water supply and has the potential to affect Central California coast steelhead trout populations. Peters Dam, which is also managed for municipal water supply, affects populations of Central California coast coho salmon and steelhead trout. Dwinnell Dam on the Shasta River potentially affects populations of Southern Oregon/Northern California coho salmon. Casitas Dam and Twitchell Dams within the range of Southern California steelhead trout.

Other dams were selected to illustrate a diversity of operations and management objectives: Woodbridge Diversion Dam on the Mokelumne River was selected to highlight potential impacts of water diversion facilities. Diversion dams often have low water storage capacities, but may divert substantial amounts of water that would otherwise flow downstream. Woodbridge also illustrates the effect of upstream dams on local operations Long Valley Dam on the Owens River impounds municipal water supplies imported from Mono Lake Basin. Though outside the range of anadromous fishes, the potentially affects several highly endemic and threatened native fish species. Boles Meadow Dam on Boles Creek impounds a small (6.2×106 m3; 5,000 acre feet), seasonal reservoir that is managed for livestock forage. The creek also supports a highly endemic and threatened natiuve fish fauna. Pine Flat Dam on the Kings River impounds one of the state’s largest reservoirs [more than 12,000×106 m3 (1,000,000 acre feet)] and is operated for multiple benefits, including flood control and agricultural water supply.

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CASE STUDY 1: BLACK BUTTE DAM

Black Butte dam is in Tehama County (Figure 21) and captures runoff from upper Stony Creek (1,916 km2), which drains the eastern slope of the Coast Range and flows into the Sacramento River, near Hamilton City. The 48-meter (156-ft) earthen dam was built in 1963 and is owned and operated by the USACE. Its operations are also coordinated with the US Bureau of Reclamation’s (USBR) and the Orland Project, which has several water storage and diversion dams in the Stony Creek watershed.

Figure 21 Black Butte Dam and catchment (1,916 km2) on Stony Creek. Downstream flows were evaluated at USGS gage #11388000 below the dam

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Aerial view of Black Butte Dam in Tehama County. Source: Army Corps of Engineers Digital Visual Library

Black Butte Dam is managed for flood control, recreation, and water supply. The dam impounds Black Butte Reservoir, with a total storage capacity of about 177×106 m3 (144,000 acre feet). A small re-regulating dam is immediately downstream. Several large dams are upstream of Black Butte Dam within the Stony Creek watershed, including East Park Dam and Stony Gorge Dam.

Black Butte Dam was included on the list of candidate dams because of observed deviation in expected monthly flows, its high cumulative impounded runoff ratio, and potential to affect threatened populations Central Valley Chinook salmon, Central Valley steelhead trout, and other sensitive fish species (Table 5).

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Table 6 Black Butte Dam on Stony Creek, Tehama County Black Butte Dam Physical Dam height: 48 m Characteristics Reservoir capacity: 1.77×108 m3 Catchment area: 1,916 km2 Mean annual inflow: 6.11×108 m3

Hydrologic Alteration Impounded runoff (IR) ratio: 0.29 ; Cumulative IR ratio: 0.50

Observed flows at downstream gage indicate a significant reduction in peak 1-day flows, enhanced summer flows and reduced late fall flows. Monthly flows follow expected seasonal patterns (r = 0.94)

Condition of Sensitive species potentially affected below dam: Central Valley fall-run, late fall-run, Downstream Fish winter-run and spring-run Chinook salmon, Central Valley steelhead trout, and hardhead

Low-flows and degraded habitat conditions may adversely affect condition of downstream native fish populations.

HYDROLOGIC CONDITIONS

Flow releases from Black Butte dam are primarily controlled for flood control and irrigation purposes. The reservoir is also managed for boating and a warm-water fishery. The USBR operates the dam April to October for irrigation and the USACE manages it for flood control from November to March (H.T. Harvey & Associates 2007).

The unimpaired annual inflow to Stony Creek at Black Butte Dam is about 6×109 m3 (50,000 acre feet), yielding an impounded runoff ratio of 0.29. When accounting for the capacity of upstream dams, the cumulative impounded runoff ratio at the dam is 0.50.

Flows observed at the USGS gage below Black Butte Dam (#11388000) were compared with modeled unimpaired hydrologic metrics. Mean annual flow below Black Butte is about 80% of its expected value, a reflection of irrigation diversions. Observed mean monthly flows (1970-1990) from January to May were slightly lower than modeled unimpaired flows, with observed-to-expected (O/E) ratios generally between 0.75 and 1.0 (Figure 22). Observed flows were similar to expected values in June and July (O/E ≈1), but were substantially higher in August and September (O/E >1.5). In the fall, mean flows below the dam were lower than expected,

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with O/E values of 0.44 in October, 0.29 in November, and 0.64 in December. Maximum 1-day peak flows have been significantly reduced, with an O/E value of 0.60. There is no evidence that flow seasonality has been altered, with observed monthly flows following expected seasonal patterns (r = 0.94).

Figure 22 Expected (E, modeled) and observed (O) mean monthly flows below Black Butte Dam and the O/E ratio

CONDITION OF DOWNSTREAM FISH POPULATIONS

Stony Creek historically supported Central Valley steelhead and spring and fall runs of Central Valley Chinook salmon. Black Butte dam completely blocked anadromous fish migration to the upper Stony Creek watershed. However, steelhead and Chinook salmon and other native fish species have been observed in lower Stony Creek, in addition to several non-native species (H.T. Harvey & Associates 2007). Sensitive fish species potentially affected by management operations downstream of Black Butte Dam include Central Valley fall- run (Status 2), late fall-run (Status 1), and spring-run Chinook salmon (Status 2, ESA-listed as threatened), and Central Valley steelhead (Status 2, ESA-listed as threatened). Stony Creek may also be important for spawning of Sacramento

CASE STUDIES | 57 sucker, Sacramento pikeminnow, and hardhead and other native fishes moving up from the Sacramento River during high flows in spring.

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

Black Butte Dam is operated to control downstream flooding and erosion in winter, and to supply irrigated farms in the summer. An Incidental Take Permit for ESA-listed salmonids in lower Stony Creek limits flood control ramping rates and minimum flow releases during the spawning period (NMFS 2008). Also, spring flow releases for salmon and steelhead are negotiated each year, based on water storage levels in Black Butte Reservoir and upstream reservoirs in the basin. Nevertheless, stream flows from late fall through spring are consistently less than levels (approximately 10-30 m3/s [400- 1,000 ft3/s]) required for spawning and incubation and to support rearing of fall-run Chinook salmon juveniles (H.T. Harvey & Associates 2007, p. 54). Low flows in the late fall are likely a critical limiting factor to salmon and other native fish taxa in lower Stony Creek.

A recent fish habitat assessment of Lower Stony Creek reported that “opportunistic use” by salmonids of Stony Creek is limited spatially and temporally because of their life cycle, the water temperature and stream flow (H.T. Harvey & Associates 2007, p. 56). Passage barriers, diversions, habitat degradation, and altered flow regimes also inhibit salmon recovery in the creek (NMFS 2008).

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CASE STUDY 2: CONN CREEK DAM

Conn Creek Dam is about 12 km (7.5 mi) upstream from the mouth of Conn Creek at its confluence with the Napa River in Napa County (Figure 23). The 38-m (125-ft) high earthen dam impounds Lake Hennessey, which has a storage capacity of 38.2×106 m3 (31,000 acre feet) and is the largest reservoir in the Napa River watershed.

Figure 23 Conn Creek Dam and catchment on Conn Creek, a tributary to Napa Creek in Sonoma County. Downstream flows were evaluated at USGS gage #11456500

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Conn Creek dam was built in 1948 by the City of Napa, which uses the reservoir as its primary municipal water source. Water is delivered to the city through the Conn Transmission pipeline. Although the dam was originally authorized as a flood control project, its operation for water supply typically results in high storage volumes and limited flood storage capacity. When the reservoir at capacity, excess flows drain from a spillway into lower Conn Creek. The dam does not have gateways or infrastructure elements to allow for controlled water releases. Conn Creek Dam was included on the list of candidate dams for its high impounded runoff ratio and potential to affect a population of threatened Central California coast steelhead trout (Table 6).

Conn Creek Dam in Napa County. Source: T. Grantham

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Table 7 Conn Creek Dam on Conn Creek, Napa County

Conn Creek Dam Physical Dam height: 38 m Characteristics Reservoir capacity: 38.2×106 m3 Catchment area: 135 km2 Mean annual inflow: 24.3×106 m3 (City of Napa, 2006); 54.2×106 m3 (model)

Hydrologic IR: 1.6, Cumulative IR: 1.6 Alteration Historic downstream flow gage indicates that natural stream drying may have occurred later in the year than under present conditions. Conn Creek below the dam currently does not have a flow gage.

Condition of Sensitive species potentially affected below dam: Central California coast Downstream Fish steelhead trout

Lack of perennial flows, low-flows, and degraded habitat conditions may adversely affect condition of downstream native fish populations.

HYDROLOGIC CONDITIONS

Mean annual inflow to Conn Creek Dam was predicted by the hydrologic model to be 54.2×106 m3 per year. The city’s water management reports estimate annual inflows at 24.3×106 m3, based on hydrologic analysis of local empirical data. Using the local estimate, Lake Hennessey (with a storage capacity of 38.2×106 m3) has an impounded runoff index of 1.6.

Flow records from a pre-dam USGS gage (#11456500) indicate a rainfall-runoff dominated hydrograph, with peak flows between January and March, followed by a low-flow period between April and November. The creek typically has intermittent flows by July and was dry from September to October, except for a few large pools. A recent stream inventory by the Napa County Resource Conservation District (Napa RCD) reported that seasonal drying of the entire channel below the dam typically occurred by mid-June (Napa RCD 2005), indicating that dam operations have resulted in lower flows in the dry season. Napa maintains storage volumes near capacity for water supply reliability. Therefore, the dam presumably does not reduce peak winter flows.

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CONDITION OF DOWNSTREAM FISH POPULATIONS

Conn Creek historically supported a run of Central California coast steelhead trout, but construction of the dam cut off access to spawning and rearing grounds in upper Conn Creek and its tributaries. Chinook salmon may have historically used the low-gradient reaches of Conn Creek for spawning and rearing. Pacific lamprey was also historically present in the Conn Creek watershed (Murphy 1949). Chinook salmon continue to spawn in the Napa River near the confluence with Conn Creek, and intermittently flowing reaches of lower Conn Creek may be used opportunistically for spawning (Napa RCD 2005). Conn Creek below the dam currently provides limited habitat for fish because of the absence of perennial flows, habitat degradation, and high summer water temperatures. Lower Conn Creek lacks summer habitat for rearing of steelhead. More tolerant native species, mainly California roach, persist in the few large pools that remain wet through the summer (Napa RCD 2005). Unlike steelhead, which require a year or more of stream residence, Chinook parr may successfully out-migrate from the creek in late spring prior to seasonal drying (Napa RCD 2005).

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

Most of the water stored behind Conn Creek Dam is diverted to the City of Napa. According to the city’s Urban Water Management Plan, about 21.5×106 m3 (or 90%) of the annual water yield at the dam is diverted (City of Napa 2006). The Plan states that the City is required to provide “sufficient releases from the reservoir to provide minimum stream flows but these requirements do not significantly affect supply reliability” (City of Napa 2006, p. 4-6). However, flows below Conn Creek Dam are not monitored and the quantity of downstream flows provided for fish is unknown.

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CASE STUDY 3: PETERS DAM

Peters Dam is in the Lagunitas Creek watershed (267 km2), which drains the western slope of the Coast Range into the Pacific Ocean at , in western Marin County (Figure 24). The dam impounds Lagunitas Creek to form Kent Lake. The Marin Municipal Water District (MMWD) manages the dam and several other reservoirs in the watershed to supply Marin County residents. Built in 1953, Peters Dam was raised by 13 meters in 1982 to increase water storage capacity to 40.5×106 m3 (33,000 acre feet), making it the largest reservoir in the watershed. Peters Dam was included on the list of candidate dams for its high impounded runoff ratio and potential to affect sensitive species in the Lagunitas Creek watershed, including Central Coast coho salmon and Central California coast steelhead trout (Table 7).

Figure 24 Peters Dam and upstream catchment (267 km2) on Lagunitas Creek in Marin County. Downstream Flows were evaluated at USGS gage #11460400

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Kent Lake and Peters Dam in Marin County. Source: K. Manohar.

Table 8 Peters Dam on Lagunitas Creek, Marin County

Peters Dam Physical Dam height: 70 m Characteristics Reservoir capacity: 40.5×106 m3 Catchment area: 56 km2 Mean annual inflow: 29.5×106 m3

Hydrologic IR: 1.3, Cumulative IR: 1.9 Alteration Observed flows at gage indicate that flows are slightly lower than under (modeled) natural conditions for most months, but that seasonal flow patterns are preserved.

Condition of Sensitive species potentially affected below dam: Central California coast Downstream Fish coho salmon, Central coast steelhead trout.

Flows are managed under an inter-agency agreement to support life history cycles of anadromous salmon and steelhead trout, and other endangered aquatic species. Degraded habitat conditions may be a primarily limiting factor for native fish populations downstream of the dam.

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HYDROLOGIC CONDITIONS

Flows in Lagunitas Creek are primarily controlled by releases from Peters Dam and natural inflow from tributaries, including San Geronimo and Devil’s Gulch creeks. Annual inflow is approximately 29.5×106 m3 per year, yielding impounded runoff values of 1.3. When accounting for the storage capacity of dams above Peters, the cumulative impounded runoff value is 1.9. This indicates that the reservoirs have the capacity to cumulatively store about twice the mean annual runoff of the upper Lagunitas Creek watershed.

Comparing modeled unimpaired hydrologic metrics with flows observed at USGS gage #11460400 below Peters Dam, mean monthly flows were slightly lower than expected values (O/E >0.7) from December to June and higher than expected (O/E =1.22 – 2.18) from July to October (Figure 25). Observed November monthly flows were about half (O/E =0.5) of expected values. Managed water releases and natural spillover events and unimpaired tributary inflows appear to maintain a seasonal hydrography in Lagunitas Creek that is similar to historic conditions (r = 0.97).

Figure 25 Expected (E, modeled) and observed monthly flow below Peters Dam on Lagunitas Creek

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CONDITION OF DOWNSTREAM FISH POPULATIONS

Lagunitas Creek watershed supports the largest remaining wild population of Central California Coast coho salmon (Status 1, ESA endangered) and an important population of Central California Coast steelhead trout (Status 2, ESA-listed as threatened). Lagunitas Creek also has one of the largest extant populations of California freshwater shrimp (ESA endangered), a species endemic to Marin, Napa and Sonoma Counties. Peters and other dams in the watershed have blocked anadromous salmonid fish passage to about 50% of their historically available habitat (MMWD 2011). Coho and steelhead continue to use 24 km (15 mi) of the creek below the dam and all accessible tributaries for spawning and rearing. The stream retains a complete native fish assemblage with relatively low numbers of non-native fish. Native fish species in the watershed include California roach, Sacramento sucker, three-spine stickleback, Pacific lamprey and at least two sculpin species.

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

The raising of Peters Dam in 1982 required State Water Resources Control Board (SWRCB) approval. Following 15 years of study and negotiations, the SWRCB issued Order WR95-17, which required MMWD to mitigate potential impacts to Lagunitas Creek fish. Pursuant to the order, the district maintains streamflow below Peters Dam to protect all life stages of coho salmon, steelhead, and California freshwater shrimp. Instream flow requirements are evaluated at the Samuel P. Taylor Park USGS gage #11460400 (Figure 21). During normal water years, minimum flow requirements range from 0.2 – 0.7 m3/s (8 – 25 ft3/s) (MMWD 2011). Because San Geronimo Creek enters Lagunitas Creek upstream of the gage, instream flow requirements may be met in part from these natural inflows, thus reducing the need to release water from Peters Dam. In the winter, substantial inflow from San Geronimo Creek makes it possible to maintain minimum releases from Peters Dam at 0.03 m3/s (1 ft3/s). In the summer, however, San Geronimo Creek flows are low (<0.03 m3/s) resulting in Peters Dam releasing virtually all flow in Lagunitas Creek (G. Andrew, personal communication).

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The managed flows release water from deep in Kent Lake and provide a consistent source of cold (<20 ºC) water for the creek, which helps maintain conditions suitable for rearing juvenile coho salmon and steelhead. In addition to minimum flow requirements that vary by season, four “upstream migration flows” of at least 1 m3/s (35 ft3/s) for three consecutive days must be provided between November and February of each year to provide for the upstream migration of adult anadromous fish.

Stream habitat degradation resulting from historic logging, along with more recent fine sediment loading and wood removal have been identified as important limiting factors to coho salmon and steelhead populations throughout the watershed (Stillwater Sciences 2008). As a result, MMWD, other agencies and local watershed groups are enhancing habitat with placement of large wood in the stream, erosion control/sediment reduction measures, riparian vegetation management, and fish passage improvements in the San Geronimo Creek drainage (MMWD 2011).

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CASE STUDY 4: WOODBRIDGE DIVERSION DAM

Woodbridge Diversion Dam is on the lower Mokelumne River in Lodi, San Joaquin County (Figure 25). The 10-m (33-ft) high dam impounds Lodi Lake, a 3.0×106 m3 (2,400 acre-foot) recreational reservoir. Water is diverted at the dam to the Woodbridge Irrigation District (WID) Diversion Canal. The dam was built in 1910 for irrigated agriculture around Lodi. Since the early 1990s, agricultural water deliveries by WID have gradually been transferred to municipal water utilities. The dam was re-built between 2006 and 2008 to improve fish passage and increase flexibility in diversion-intake and downstream flow-release operations.

Figure 26 Woodbridge Diversion Dam and catchment (1,682 km2) on the Mokelumne River, San Joaquin County; inset map shows large upstream dams and USGS gages above the dams (#11319500), below Camanche Dam (#11323500), and below Woodbridge Dam (#11325500)

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Woodbridge Dam was included on the list of candidate dams for its high cumulative impounded runoff ratio, evidence of monthly and peak flow alteration and its potential to affect sensitive populations of Central Valley Chinook salmon and Central Valley steelhead (Table 8).

Woodbridge Diversion Dam on the Mokelumne River, San Joaquin County. Source: G. .

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Table 8 Woodbridge Diversion Dam on the Mokelumne River, San Joaquin County

Woodbridge Diversion Dam Physical Dam height: 10 m Characteristics Reservoir capacity: 3.0×106 m3 Catchment area: 1,682 km2 Mean annual inflow: 9.5×108 m3

Hydrologic IR: <0.01, Cumulative IR: 1.1 Alteration Flows are substantially lower than natural conditions in the winter and spring because of large upstream dam and diversion operations. Peak flows have also been greatly reduced. Despite the overall reduction in flow magnitudes, monthly seasonal flow patterns have been preserved.

Condition of Sensitive species potentially below dam: fall-run Central Valley Chinook Downstream Fish salmon, Central Valley steelhead, southern green and white sturgeon.

Low-flows and associated water quality degradation limit successful rearing of juvenile anadromous fish below dam.

HYDROLOGIC CONDITIONS

Mokelumne River inflows to Woodbridge are completely regulated by large upstream dams. The total storage capacity of Camanche Dam (5.2×108 m3), Pardee Dam (2.6×108 m3), Salt Springs Dam (1.8×108 m3), and other smaller dams upstream of Woodbridge is 10.5×108 m3, equivalent to 110% of the Mokelumne’s annual flow. The East Bay Municipal Water District (EBMUD) operates Pardee Dam in conjunction with Camanche Dam for flood control and water supply for Oakland, Berkeley, and other Area communities. EBMUD has a water right to divert up to 325 million gallons per day, or up to 4.5×108 m3 per year, from the Mokelumne River at Pardee Dam. Based on flows measured at USGS stations above and below Pardee Dam, 30% (or 2.5×108 m3) of annual inflow of the Mokelumne River is diverted on average (1963-2011). An additional 1.9×108 m3 is diverted from the river at Woodbridge Dam. As a result, observed annual flow below Woodbridge is approximately 50% of the river’s natural unimpaired flow. The operation of Woodbridge and larger upstream dams has resulted in significant reduction in annual discharge, lower peak flows, and decreased flow variability.

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This is illustrated by the 2010 hydrograph at USGS gages upstream of Pardee Dam, downstream of Camanche Dam, and downstream of Woodbridge (Figure 27).

Figure 27 Observed daily discharge in the Mokelumne River for the 2010 water year, above Pardee Dam, downstream of Camanche Dam, and below Woodbridge Dam

Overall, flows in the Mokelumne River below Woodbridge Dam are controlled at lower and more stable levels than occurred under natural conditions. Observed mean monthly flows in the winter and spring (Jan – Jun) are about 50% of expected values (Figure 27), and are closer to expected values in October and November during the river’s natural low-flow period. Although flows have been substantially reduced below Woodbridge, the correlation between observed and expected monthly flows is high (r = 0.95), indicating that general seasonal patterns in monthly flows are preserved, albeit at substantially lower magnitudes (Figure 28). The observed maximum annual 1-day flood is about 25% of the expected values. The significant decrease in flood flow magnitudes in the lower Mokelumne is consistent with reports in previous studies. Kondolf and Batalla (2005) found that the Q2 (2-year return interval flood) has been reduced by 80% and the Q10 by 75% after construction of major dams on the Mokelumne River; and Merz and Setka (2004) determined that after the construction of

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Camanche Dam, annual peak flows have never exceeded 200 m3/s, while pre-dam peak flows were greater than 200 m3/s in 21 of 57 years.

Figure 28 Expected (E, modeled) and observed mean monthly flow below Woodbridge Dam on the Mokelumne River

CONDITION OF DOWNSTREAM FISH POPULATIONS

Sensitive fish species potentially affected by operations at Woodbridge Dam include Central Valley fall-run Chinook salmon (Status 2) and Central Valley steelhead (Status 2, ESA- listed as threatened). Southern green sturgeon (Acipenser medirostris, Status 1, ESA-listed as threatened) and white sturgeon (Acipenser transmontanus, Status 2) may also be present. Populations of Central Valley Chinook salmon and hatchery steelhead are the subject of on-going monitoring and restoration efforts. They are maintained by artificial production at the Mokelumne River Fish Hatchery at Camanche Dam, an impassable barrier. A fish passage facility at Woodbridge Dam allows access to salmon and steelhead spawning habitat below Camanche.

Rearing of juvenile steelhead trout has been observed in wet years, when flow releases below Woodbridge are greatest (NMFS 2002). But in dry years, downstream habitat conditions are so poor that out-migrating juvenile salmon smolts are

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captured at Woodbridge and transported by truck to a release location in the Delta. Habitat and flow alterations in the lower Mokelumne have promoted non-native species such as western mosquito fish (Gambusia affinis), golden shiner (Notemigonus crysoleucas), spotted bass (Micropterus punctulatus) and striped bass (Morone saxatilis). Abundant native species include Sacramento sucker (Catostomus occidentalis), Sacramento pikeminnow (Ptychocheilus grandis), tule perch (Hysterocarpus traski), and prickly sculpin (Cottus asper). The combined diversity of native and non-native fish species in the Mokelumne River is greatest in the reaches below Woodbridge Dam, presumably because of the effects of tidal action and influence of tributary waterways (Merz and Saldate 2004).

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

Flow releases to the Mokelumne River below Camanche and Woodbridge Dams are dictated in a 1998 Joint Settlement Agreement (JSA) between EBMUD, U.S. Fish and Wildlife Service and California Department of Fish and Wildlife. Minimum required flow releases are designed to support anadromous salmon, including adult upstream passage and outmigration of juveniles. The amount of water released at Camanche (and diverted at Woodbridge) depends on the season and the water year. Based on a 10-year review of the JSA, actual flows have always exceeded the required releases below Camanche and Woodbridge dams (EBMUD et al. 2008). However, low summer flows, high water temperatures, and degraded habitat limit salmonids in most years.

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CASE STUDY 5. TWITCHELL DAM

Twitchell Dam is on the Cuyama River, a tributary to the River in southern San Luis Obispo and northern Santa Barbara counties (Figure 29). The dam impounds the 290×106 m3 (235,000 acre feet) Twitchell Reservoir. The Bureau of Reclamation built the dam in 1956 for water conservation, irrigation, and flood control. It was designed primarily to provide relatively short-term storage and releases of flows from the Cuyama River to replenish the Santa Maria Valley groundwater basin. The dam is operated by Santa Maria Valley Water Conservation District. It was included on the list of candidate dams for its large impounded runoff ratio and potential to affect endangered Southern California steelhead trout populations (Table 9).

Figure 29 Twitchell Dam and catchment (2,888 km2) on the Cuyama River, in southern San Luis Obispo and northern Santa Barbara counties

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Twitchell Dam on the Cuyama River. Source: US Bureau of Reclamation.

Table 9 Twitchell Dam on the Cuyama River, San Luis Obispo and Santa Barbara counties

Twitchell Dam Physical Dam height: 64 m Characteristics Reservoir capacity: 290×106 m3 Catchment area: 2,888 km2 Mean annual inflow: 64.5×106 m3 (empirical), 1,043×106 m3 (model)

Hydrologic IR: 4.5, Cumulative IR: 4.5 Alteration

Condition of Sensitive species potentially below dam: Southern California steelhead Downstream Fish trout, arroyo chub

Low-flows may limit successful passage of steelhead trout through the Santa Maria to spawning reaches.

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HYDROLOGIC CONDITIONS

Twitchell Dam captures surface runoff from the 2,888-km2 (1,115-mi2) Cuyama River basin. Inflows are intermittent and highly variable, but yielded an annual average runoff of 64.5×106 m3 from 1967-2010 (City of Santa Maria 2010). The dam has capacity to capture all inflow in most years (IR = 4.5), but is operated to release water relatively quickly, such that the reservoir is often dry in the summer and fall. Releases are controlled to prevent surface-water reaching the Pacific Ocean, maximizing potential percolation into the downstream Santa Maria groundwater basin. Predictions of expected mean flows by the hydrologic model are unreliable for the Cuyama River because of the high inter-annual variability of flow patterns. Model predictions of mean annual flows were about 16 times greater than observed values. Therefore, deviation of observed from expected (modeled) flow metrics was not assessed. A recent instream flow study on the Santa Maria River found that Twitchell Dam has had no detectable effect on overall patterns of annual no-flow and peak-flow conditions, but has altered the timing and frequency of intermediate flows in both the Cuyama and Santa Maria rivers (Stillwater Sciences and Kear Groundwater 2012).

CONDITION OF DOWNSTREAM FISH POPULATIONS

The Santa Maria River watershed continues to support Southern California steelhead trout, listed as endangered under the federal ESA. Both steelhead trout (anadromous O. mykiss) and (resident O. mykiss) historically occurred in the Cuyama River. The extent of historical steelhead occurence in the Cuyama River watershed above Twitchell Dam is unknown, but was likely confined to perennial tributaries of the upper river basin (Stillwater Sciences and Kear Groundwater 2012). The majority of suitable habitat for steelhead occurs in the Sisquoc River watershed (Figure 29), which is smaller than the Cuyama but is not dammed and has higher flows.

Steelhead spawning in the Cuyama River below Twitchell Dam has not been documented. Releases from Twitchell, however, could influence the upstream migration of steelhead through the Santa Maria River to suitable spawning areas in the

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Sisquoc River and perennially flowing tributaries (Stillwater Sciences and Kear Groundwater 2012). Arroyo chub (Gila orcuttii, Status 2) may also be present in the Santa Maria River watershed and could be affected by the operation of Twitchell Dam.

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

Twitchell Dam is primarily managed for groundwater recharge without regard for the downstream flow needs of fish (Twitchell Management Authority & MNS Engineers 2010). Although the Cuyama River reach immediately below the dam historically provided limited suitable habitat for O. mykiss and other native fishes due to its ephemeral nature, intermittent flows from the Cuyama improve fish passage opportunities through the Santa Maria to the Sisquoc River (Stillwater Sciences and Kear Groundwater 2012). There is evidence that current flow management at Twitchell Dam has increased the frequency of flows that trigger upstream steelhead movement. But the flows are too brief for successful migration (Stillwater Sciences and Kear Groundwater 2012). Adult steelhead that begin their upstream migration under favorable flow conditions now run a greater risk of being stranded.

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CASE STUDY 6. LONG VALLEY DAM

Long Valley dam impounds the 226×106 m3 (183,500 acre-feet) Crowley Lake on the Owens River in southern Mono County (Figure 30). The 38-m (126-ft) earthen dam was built by the Los Angeles Department of Water and Power (LADWP) in 1941 to supply the . It is the largest reservoir in the Los Angeles water system. The dam is also managed for flood control, hydroelectric power production and recreation.

Figure 30 Long Valley Dam and catchment (994 km2) on the Owen River, Mono County

Long Valley Dam was included on the list of candidate dams for its high cumulative impounded runoff ratio and potential to affect sensitive native species populations, including the endemic Owens tui chub (Siphatales bicolor snyderi, Status 1) (Table 10). Owens speckled dace (Rhinichthys osculus, Status

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1) appears to have been lost from dam’s HUC12 watershed, but its current range encompasses tributaries of the Owens River downstream of the dam.

Long Valley Dam at the head of Owens Gorge impounds the Owens River to form Crowley Lake. Source: S. Volpin.

Table 10 Long Valley Dam on the Owens River, Mono County

Long Valley Dam Physical Dam height: 38 m Characteristics Reservoir capacity: 226×106 m3 Catchment area: 994 km2 Mean annual inflow: 193×106 m3 (modeled)

Hydrologic IR: 1.2, Cumulative IR: 1.2 Alteration

Condition of Sensitive species potentially below dam: Owens tui chub, Owens speckled Downstream Fish dace

Native species lost from HUC12 watershed below dam: Owens speckled dace

Non-native species, population fragmentation, and habitat degradation may adversely affect condition native fish.

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HYDROLOGIC CONDITIONS

Long Valley Dam impounds a 994-km2 (383-mi2) catchment of the Owens Rivers, which is fed by runoff and springs. Inflows to the dam are augmented by the Mono Craters Tunnel (Figure 27) and the Rock Creek Diversion. A 1998 Water Rights Order (WR 98-05), allows an annual import through the tunnel of 19.7 ×106 m3 (16,000 acre feet), about a 10% increase in natural inflows to the reservoir. The impounded runoff ratio of Long Valley Dam is 1.2, excluding inflows from the tunnel. It is 1.1 if the augmented flows are included.

No direct downstream discharge is permitted from Long Valley Dam. All flows purposely bypass a 10-mile long reach designated as critical habitat for Owens tui chub to prevent introduction of genetically introgressed tui chub from Crowley Lake. Flows in the 10-mile reach are maintained by leakage from the earthen dam and inflows from spring-fed tributaries. The next 10 river miles are managed for non-native trout and riparian habitat, through flows from a power plant. Most flows continue to bypass the Owens River Gorge through three power plants before being spilling into a small reservoir serving hydroelectric operations.

Long Valley Dam operations affect Owens River flows for approximately 90 km (60 mi) to the Tinemaha Dam reservoir, immediately upstream of Los Angeles Aqueduct intake. Flows in the affected river reach have truncated peak volumes, consistently reduced minima, and seasonally delayed high flows (Hickson and Hecht 1992; Smeltzer and Kondolf 1999).

CONDITION OF DOWNSTREAM FISH POPULATIONS

The Owens River historically supported a diverse assemblage of native endemic fish species, including the Owens tui chub, Owens specked dace, Owens pupfish, and Owens sucker (Catostomus fumeiventris). Human activities, including major Los Angeles water development projects, have caused the decline of chub, dace, pupfish and other rare species in the river basin (U.S. Fish and Wildlife Service 1998). With the exception of the Owens sucker (Deinstadt and Parmenter 1997), the basin’s endemic fish populations have become entirely displaced from the Owens River by introduced predatory fishes.

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The Owens tui chub is listed as endangered under both federal and state ESAs. Once widespread and abundant in the basin, the fish is currently confined to isolated sites, including a section of Owens Gorge downstream of Long Valley Dam designated as critical habitat (50 Federal Register 31593- 31597). Owens specked dace (Status 1) and Owens pupfish (Status 1) also historically occurred in the river upstream and downstream of the dam. The historic northern limit of the pupfish (Status 1) occurred at the approximate site of Pleasant Valley Dam, 25 river miles below Long Valley Dam. Also, several alien game fish species have established permanent populations in Crowley Reservoir and Owens River, including a productive brown trout fishery.

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

Long Valley Dam is primarily managed for water supply for Los Angeles, with secondary power generation objectives. Flows for fish are not considered in its operations. However, artificial low flows below the dam appear to sustain an Owens tui chub population in parts of the designated critical habitat. Further downstream, hydroelectric diversions have historically left the river partially or completely dewatered between the power plants (City of Los Angeles 2010). Los Angeles initiated a restoration project to improve flows for threatened fish species between the plants in the downstream half of the gorge in response to a 1991 state Fish and Game lawsuit over potential violations of Section 5937 (City of Los Angeles 2010).

The proposed Owens Gorge Restoration Project involves a modified schedule of flow releases through Owens Gorge that provides improved base flows for sustaining brown trout and seasonal pulse flows for riparian recruitment and channel maintenance. The management of Crowley Lake for water delivery and flood control is not affected by the project (City of Los Angeles 2010), and the potential effects of Long Valley Dam operations on downstream fish has not been evaluated. Los Angeles is working with U.S. Fish and Wildlife Service, California Department of Fish and Wildlife, and other state and federal agencies to approve and implement the Owens Gorge Restoration Project (LADWP 2013).

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CASE STUDY 7. CASITAS DAM

Casitas Dam is on Coyote Creek, approximately 5 km (3 mi) above its confluence with the Ventura River in Ventura County (Figure 30). The 102-m (334-ft) earth-fill dam impounds the 313×106 m3 (254,000 acre-feet) Lake Casitas (USBR 2013). The reservoir captures inflow from the 105-km2 (41 mi2) Coyote Creek watershed and imported water delivered by canal from the Robles Diversion Dam on the upper Ventura River (Figure 31). Outlet works at Casitas Dam convey water to the Casitas Municipal Water District (CMWD) service area. The district manages the reservoir for irrigation and water supply for approximately 60,000 people (Latousek 1995).

Figure 31 Casitas Dam and catchment (105 km2) on Coyote Creek, a tributary to the Ventura River, Ventura County

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Casitas Dam was included on the list of candidate dams because its high impounded runoff index and potential effects on sensitive populations of Southern California steelhead trout and arroyo chub (although the chub is not native to the Ventura River) (Table 11).

Aerial view of Casitas Dam on Coyote Creek, Ventura County. Source: US Bureau of Reclamation.

Table 11 Casitas Dam on Coyote Creek, Ventura County

Casitas Dam Physical Dam height: 102 m Characteristics Reservoir capacity: 313×106 m3 Catchment area: 105 km2 Mean annual inflow: 17.9×106 m3 (model, 1970-2000), 11.1×106 m3 (observed, 1928-1955); 16.1×106 m3 is imported from the Ventura River water from Robles Diversion Dam

Hydrologic IR: 17.5, Cumulative IR: 17.5 (based on modeled Coyote Creek inflow) Alteration

Condition of Sensitive species potentially below dam: Southern California steelhead trout, Downstream Fish arroyo chub

Lack of perennial flows, low-flows, and degraded habitat conditions adversely affect condition of downstream native fish populations.

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HYDROLOGIC CONDITIONS

Casitas Dam has the capacity to capture almost 20 times the natural inflow from Coyote Creek; natural mean annual inflow to the 313×106 m3 reservoir was predicted to be 17.9×106 m3. Pre-dam flow records (USGS #11118000, 1928-1955) indicate that annual flow was slightly lower (11.1×106 m3) than model predictions. Flows on Coyote Creek are not currently monitored by USGS. Historic records, however, show natural flows with strong seasonality and interannual variability. Annual runoff, which varied historically between 0.06-63×106 m3 per year, was delivered between January and March, followed by intermittent flows from June through October (Figure 29). After Coyote Creek was dammed in the mid-1950s, flows declined to 2.5×106 m3 per year, on average (1969-1982). Post- dam monthly flows (1969-1982) were 3-30% of pre-dam flows (Figure 31). Current water imports from the Robles-Casitas Canal vary with available runoff, averaging 16.1×106 m3 (13,095 acre feet) per year (Cardno ENTRIX 2012). Flows in the lower Ventura River are about 50% of their natural, unimpaired levels due to Casitas Dam and associated facilities (Cardno ENTRIX 2012). Nearly all outflow from the dam is exported. As a result, Coyote Creek below the dam is usually dry (California RWQCB 2002).

Figure 32 Mean monthly flows on Coyote Creek before and after construction of Casitas Dam, assessed at USGS gage #11118000

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CONDITION OF DOWNSTREAM FISH POPULATIONS

Historically, Coyote Creek was one of the most important tributaries in the Ventura River watershed for steelhead trout production (NMFS Service 2003). Construction of Casitas Dam completely blocked access to spawning and rearing habitat in Coyote Creek (Becker et al. 2010). The 5-km (3-mi) reach below the dam does not currently support fish because of low flows and degraded habitat. Releases from the dam, however, could allow steelhead to migrate through the lower Ventura River. Arroyo chub are in the Ventura River near its confluence with Coyote Creek and could also benefit from improved flows from Casitas.

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

Casitas Dam primarily supplies water for irrigation and municipal needs. There are no required flow releases from Casitas for fish. The downstream channel is typically dewatered. Steelhead in the Coyote Creek basin historically spawned above Casitas Reservoir. Lower Coyote Creek is in poor condition because of chronic streambank erosion and insufficient storm-flushing flows (NMFS 2003). Flow releases from Casitas could potentially benefit steelhead trout migrating through the lower Ventura River and improve habitat for other native fish species, including the arroyo chub. A biological opinion for Robles Diversion Dam sets conditions for to minimize impacts on steelhead trout in the Ventura River, but does not address the potential benefits of improving downstream flows in Coyote Creek below Casitas Dam (NMFS 2003).

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CASE STUDY 8. BOLES MEADOW DAM

Boles Meadow Dam is on Boles Creek, a major tributary to Reservoir in the upper Lost River watershed of northwest Modoc County (Figures 33). The 2.5-m (8-ft) earthen dam impounds runoff from the Boles Creek watershed [692 km2 (267 mi2)]. The dam is owned by the U.S. Forest Service (USFS), which manages the 6×106 m3 (5,000 acre-foot) reservoir for irrigation and forage production.

Figure 33 Boles Meadow dam and catchment (692 km2) on Boles Creek, Modoc County

Boles Meadow Dam was included on the list of candidate dams because of its large cumulative impounded runoff ratio and the potential presence of several sensitive species downstream of the dam: the Lost River sucker (Catostomus luxatus, Status 1), shortnose sucker (Chasmistes breviostris, Status 1), and

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Klamath largescale sucker (Catostomus snyderi, Status 2) (Table 12).

Aerial view of Boles Meadow dam during spring runoff on Boles Creek, Modoc County. Source: C. Ellsworth.

Table 12 Boles Creek Dam on Boles Creek, Modoc County.

Boles Creek Dam Physical Dam height: 2.5 m Characteristics Reservoir capacity: 6.2×106 m3 Catchment area: 692 km2 Mean annual inflow: 16.9×106 m3

Hydrologic IR: 0.4, Cumulative IR: 1.2 Alteration

Condition of Sensitive species potentially below dam: Lost River sucker, shortnose Downstream Fish sucker, Klamath largescale sucker, upper Klamath marbled sculpin

Low-flows and habitat degradation may adversely affect condition of fish downstream. Seasonal impoundment may disrupt migration of sucker.

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HYDROLOGIC CONDITIONS

Boles Creek, a tributary to Clear Lake Reservoir, feeds the Federal Klamath Irrigation Project (USFS 2012). The creek has no USGS gages and little published on its hydrology or potential effects of impoundments. Tate et al. (2007) described Boles Creekas “intermittent during the summer months creating large, isolated stream reaches or pools characterized by bedrock-basalt substrate” underlying the Modoc Plateau. Base flows naturally remain low through fall and winter and peak during spring snowmelt, typically between April and June, based on reports from other streams in the region. Estimated total annual inflow at Boles Meadow Dam is 16.9×106 m3 (13,700 acre-feet) per year, yielding an IR of 0.4. The CIR for Boles Meadow is 1.2 when accounting for the total storage capacity [20.9×106 m3 (16,900 acre-feet)] of all reservoirs in the catchment (Figure 33). Therefore, reservoirs in the system have the capacity to capture a significant proportion of the catchment’s annual runoff, indicating the potential for significant downstream hydrologic alteration at Boles Meadow Dam, particularly during spring runoff.

CONDITION OF DOWNSTREAM FISH POPULATIONS

Clear Lake and the upper Lost Creek watershed historically supported an assemblage of endemic fishes, including several species of sucker. Both the Lost River and shortnose sucker were abundant in the Lost River drainage and were the most important food fish for Native Americans of the Klamath Lakes region ( 1898). The Klamath River sucker is uncommon to the Lost Creek system but may occasionally be present (Koch and Contreras 1973). The draining and eutrophication of lakes in the upper Klamath river system, overfishing and degradation of tributary habitats from cattle grazing and water diversions have all contributed to the decline of Lost River sucker and shortnose sucker populations (Moyle 2002). The Lost River and shortnose sucker are listed as endangered under federal and state ESAs. Clear Lake populations of Lost River and shortnose suckers spawn in Boles Creek and other tributary streams in the spring (Moyle 2002). Fish surveys from the 1970s found shortnose sucker in Boles Creek (Koch et al. 1975). The extent to which sucker populations of Clear Lake

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currently use Boles Creek for spawning is unknown. Other native species previously recorded in the creek include the upper Klamath marbled sculpin (Status 3), blue chub, tui chub, and speckled dace (Koch et al. 1975).

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

Boles Meadow Dam is operated to create a seasonal reservoir to irrigate livestock forage (USFS 2005). There is no evidence that effects on fish are considered in its operation. The dam impounds spring flows, thereby reducing flows downstream. However, moderate to high flows likely spillover the 2.5-m dam. Such impoundments could be expected to delay re- watering of the downstream channel in spring and accelerate the downstream flow recession in summer, potentially disrupting out-migration of adults and juvenile species from tributary streams to Clear Lake (S. Reid, personal communication). Therefore, seasonal timing of reservoir filling and drawdown at Boles Meadow Dam could be potentially modified to benefit the condition of fish downstream.

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CASE STUDY 9. PINE FLAT DAM

Pine Flat Dam on the Kings River in Fresno County stands 134-m (440-feet) high and stores up to 1,233×106 m3 (1,000,000 acre feet), making it one of the largest reservoirs in California (Figure 34). The Army Corps of Engineers built the dam in 1954 for flood protection and secondarily for irrigation, hydroelectric power, and recreation, including a trout fishery. Pine Flat Dam was included on the list of candidate dams because of evidence of monthly flow alteration, a high impounded runoff ratio, the potential harm Kern brook lamprey (Lampetra hubbsi, Status 2), and the loss of sensitive fish species from their historic range, including Central Valley spring-run Chinook salmon (Status 2), Central Valley fall-run Chinook salmon (Status 2), and Central Valley steelhead (Status 2) (Table 13).

Figure 34 Pine Flat Dam and catchment (4,000 km2) on the Kings River in Fresno County. Flows were evaluated at USGS gage #11221500

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Pine Flat Dam on the Kings River, Fresno County. Source: Wikipedia under GNU Free Documentation License.

Table 13 Pine Flat Dam on the Kings River, Fresno County.

Pine Flat Dam Physical Dam height: 134 m Characteristics Reservoir capacity: 1,233×106 m3 Catchment area: 4,000 km2 Mean annual inflow: 1,506×106 m3

Hydrologic IR: 0.8, Cumulative IR: 1.0 Alteration Observed flows at downstream gage indicate a significant reduction in peak 1-day flows, reduced fall and winter flows, and enhanced summer flows. Monthly flows follow deviate slightly from expected seasonal patterns (r = 0.79)

Condition of Sensitive species potentially below dam: Kern brook lamprey Downstream Fish Species lost from HUC12 watershed affected by dam: Central Valley fall- run and spring-run Chinook salmon, Central Valley steelhead

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HYDROLOGIC CONDITIONS

The unimpaired annual inflow of the Kings Rivers at Pine Flat Dam is about 1,506×106 m3 (1,221,000 acre feet) yielding an impounded runoff ratio of 0.8. There are several other dams in the 4,000-km2 (1,544-mi2) catchment above Pine Flat, which have a total storage capacity of about 303×106 m3 (246,000 acre feet), yielding a cumulative runoff ratio of 1.0. Observed flows at the USGS gage #11221500 below Pine Flat Dam were compared with modeled, unimpaired hydrologic metrics. Observed mean monthly flows were generally lower than expected values in the late fall and winter (November – March) and in the spring (April – June) (Figure 35). The most notable deviation from expected patterns was in the summer and early fall (July – October), when observed monthly flows were estimated to be 1.5-2 times greater than expected values. Overall, there was moderate deviation from expected seasonal flow patterns (r = 0.79). Observed maximum 1-day flows were about 50% of expected values, reflecting the dams flood-control operations.

Figure 35 Expected (E, modeled) and observed mean monthly flows below Pine Flat Dam on the Kings River

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CONDITION OF DOWNSTREAM FISH POPULATIONS

Spring- and fall-run Chinook salmon historically occurred at least periodically in the Kings River, when floodwaters in the Basin spilled into the San Joaquin River system, providing access for fish to the Kings River. Salmon would ascend the Kings River and spawn up to the mouth of the (Yoshiyama et al. 2001). Water diversions for farmers resulted in the extirpation of salmon runs in the Kings and upper San Joaquin rivers by the mid-20th century (Yoshiyama et al. 2001). The Kern brook lamprey (Lampetra hubbsi) is an endemic species to the San Joaquin River Basin. Relatively little is known about the life history and historic distribution of the lamprey (Moyle 2002). Known populations are isolated and include a Kings River population above and below Pine Flat Dam. The risk of local extirpation is high because of the lamprey’s fragmented distribution and occurrence below dams that are operated with limited regard to their flow needs. The lower river also supports Sacramento pikeminnow, Sacramento sucker, and two species of sculpin, but the population status of these species in the river is not known.

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

The Army Corps operates Pine Flat Dam to reduce flood flows in the spring, and enhance flows in the summer for agricultural irrigation. In 1964, CDFW entered an agreement with the Water Association (KRWA) and Kern River Conservation District (KRCD) to secure minimum flow releases below Pine Flat Dam, primarily to restore a trout fishery. In the 1990s, modifications to the Pine Flat Dam and downstream power plant were made to better control the temperature of outflows to the river. These changes were followed by the development of the Kings River Fisheries Management Program, which established new agreements between CDFW and facility operators at Pine Flat and upstream dams to improve the quantity and quality (i.e., temperature) of downstream flow releases for trout (KRCD and KRWA 2003).

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CASE STUDY 10. DWINNELL DAM

Dwinnell Dam is on the Shasta River in Siskiyou County (Figure 36). The dam impounds the 62×106 m3 (50,000 acre- feet) Dwinnell Reservoir, also known as Lake Shastina. The reservoir was constructed in the late 1920s as a water supply project for the Montague Water Conservation District (MWCD). The reservoir is fed by inflows from the Shasta River and a diversion from Parks Creek, about 2 km (1.2 mi) upstream from the reservoir. MWCD owns Dwinnell Dam and operates it primarily to irrigate pasture.

Figure 36 Dwinnell Dam and catchment (142 km2) on the Shasta River, Siskiyou County

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Dwinnell Dam was included on the list of candidate dams because of its high impounded runoff index and its potential effects on sensitive species populations, including ESA-listed Southern Oregon/Northern California coast coho salmon (Status 1), Upper Klamath-Trinity fall run Chinook salmon (Status 2) and Klamath Mountain Province winter steelhead (Status 3) (Table 14).

Dwinnell Dam on the Shasta River, Siskiyou County. Source: S. Harding/Klamath Riverkeeper.

Table 14 Dwinnell Dam on the Shasta River, Siskiyou County.

Dwinnell Dam Physical Dam height: 29 m Characteristics Reservoir capacity: 61.7×106 m3 (50,000 acre feet) Catchment area: 142 km2 (55 mi2) Mean annual inflow: 74×106 m3 (empirical); 188×106 m3 (model)

Hydrologic IR: 0.81, Cumulative IR: 0.81 (based on empirical inflow estimates) Alteration

Condition of Sensitive species potentially below dam: Southern Oregon/Northern Downstream Fish California coho salmon and Upper Klamath-Trinity fall run Chinook salmon

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HYDROLOGIC CONDITIONS

Dwinnell dam impounds the 370 km2 (143 mi2) upper Shasta River watershed. The reservoir receives annual inflows of about 74×106 m3 (60,000 acre feet) per year, including imported water from an upstream diversion on Parker Creek (Vignola and Deas 2005). This is significantly lower than model predictions of 188×106 m3 per year. Based on the lower annual inflow estimate, the dam has an IR value of 0.81. There are no large dams present in the upstream catchment, so the cumulative IR is essentially the same as the IR.

Outflows from the reservoir include controlled and uncontrolled releases to the Shasta River and controlled releases to the MWCD irrigation canal (Figure 36). Observed monthly flows were not compared with expected values because of the poor predictive performance of the model for the Shasta River. Previous studies, however, have documented significant reductions in Shasta River flows relative to simulated, unimpaired conditions. For example, Null et al. (2010) reported that current flow releases below Dwinnell Dam are limited to 0.05 m3/s because of leakage, with summer releases up to 0.25 m3/s to fulfill downstream water rights, compared with simulated unimpaired baseflows of 1-4 m3/s. Null et al. (2010) also reported that the dam captured all inflows from the upper Shasta River and Parks Creek in most years and, as a result, downstream flows showed only modest peaks from storm runoff.

CONDITION OF DOWNSTREAM FISH POPULATIONS

The Shasta River historically supported healthy populations of Chinook salmon, coho salmon, and steelhead trout. It was one of the most productive tributaries in the Klamath River Basin. Dwinnell dam blocked salmon and steelhead passage to approximately 22 percent of historical spawning and rearing habitat in the Shasta River Basin (CDFW 2012). Declining annual returns of salmon to the Shasta have tracked range- wide population declines over the past several decades (Moyle 2002). Below the dam, habitat conditions for salmon and steelhead have been degraded by low-flows and high water temperatures (Null et al. 2010), although these conditions are only partially attributable to Dwinnell Dam. Other native

96 | RESTORING FLOWS FOR FISH BELOW DAMS

species potentially present in the Shasta below Dwinnell Dam include Pacific lamprey, Klamath River lamprey, Klamath River speckled dace, and Klamath small-scale sucker (Deas et al. 2004).

MANAGEMENT OF DOWNSTREAM FLOWS FOR FISH

Most of the water impounded by Dwinnell Dam is released to the MWCD irrigation canal, resulting in year-round flow impairment to the Shasta River. During the irrigation season, flows released from the dam into the Shasta River are typically limited to 0.25 m3/s to fulfill downstream water rights (Null et al. 2010). However, changes in dam operations are likely to occur in the future, following recommendations of a recent instream flow assessment on the Shasta River (McBain and Trush 2013). The recommendations are intended keep fish in good condition, as Fish and Game Code 5937 requires. They include increased summer flows to maintain suitable water temperatures and high-pulse spring releases to promote salmon smolt outmigration.

CASE STUDIES | 97

CASE STUDY FINDINGS

These case studies provide preliminary, site-specific investigations of dam operations and their potential effects on downstream fish. Indicators of hydrologic alteration and fish population impairment used in the systematic evaluation of dams generally corresponded with site-specific reports of environmental conditions and downstream effects of the case study dams.

All of the dams were confirmed to have evidence of downstream impacts to sensitive fish populations. For dams with reliable downstream flow gages, there was direct evidence of hydrologic alteration. For other dams, qualitative descriptions of hydrologic impacts from technical reports and interviews indicated that flows below dams also deviated in some way from expected, unimpaired conditions. The case studies found some limitations in the hydrologic model used to predict annual flows, particularly for intermittent streams in arid regions (e.g., Cuyama Creek and Conn Creek). However, locally derived estimates of annual flows were generally available in published reports.

Several of the case study dams are subject to some form of environmental flow requirements, for example, the biological opinion for Stony Creek, the Joint Settlement Agreement for the Mokelumne River, and the state water board order for Lagunitas Cree. Also, Section 5937 has been considered in identifying flow needs for fish below Long Valley Dam, Peters Dam and Dwinnell Dam. For Peters Dam, the summer flow releases are apparently responsible for maintaining Lagunitas Creek as an important refuge for threatened coho salmon and other cold-water species.

Other dams appear to have limited or no protections of downstream flows for sustaining fish, including Conn Creek, Boles Meadow, Casitas, Twitchell and Dwinnell. Current efforts to assess environmental flow needs in the Santa Maria and Shasta River suggest that the management of flow releases for fish below Twitchell and Dwinnell may be improved.

Operations of the case study dams were influenced by a diverse and complex suite of legal and institutional factors, involving

98 | RESTORING FLOWS FOR FISH BELOW DAMS

local water districts, multiple state and federal agencies and private parties. The studies also showed that dam operations and their consequent effects on downstream flows were often affected by other dams and diversions located up- and downstream. Inflows and operations of the Woodbridge Diversion Dam, for example, are completely dependent on management of major upstream dams under separate ownership. The highly integrated nature of water management projects suggests that modifications to dam operations to provide Section 5937 flows would require working not only with the owner/operators of the dam, but also with operators of other water works in the river basin.

For the case study dams, observed downstream flow alteration was generally coupled with significant downstream habitat alteration. The degradation of habitat was associated with direct effects of the dam (e.g., downstream channel incision from the loss of sediment inputs) and indirect effects (e.g., land use development along the stream corridor facilitated by the reduction in flood risk). The poor habitat conditions below many dams suggest that improving flows for fish may also require habitat restoration to maintain fish in good condition. In addition, the presence of non-native species may preclude the recovery of native fish populations (Moyle and Mount 2007), although the success of a managed environmental flow regime to suppress alien fishes is a hopeful sign (Kiernan et al. 2012). Therefore, outcomes of restoring Section 5937 flows are likely to be influenced by many physical and ecological factors that warrant careful consideration.

Overall, the case studies showed that each dam has a unique set of management constraints, jurisdictional issues, and environmental factors that must be addressed in the context of Section 5937. This is probably true of all dams. We recommend that site-specific analyses presented in the case studies be done for every high-priority dam identified in this study.

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APPENDIX A

SENSITIVE NATIVE FISH SPECIES LIST

California native fish species with sensitive (at risk, vulnerable, or near-threatened) population status, per Moyle et al. (2011).

Common Name Scientific Name Conservation Status

Goose Lake lamprey Entosphenus tridentata 2-Vulnerable Kern brook lamprey Lampetra hubbsi 2-Vulnerable Northern green sturgeon Acipenser medirostris 2-Vulnerable Southern green sturgeon Acipenser medirostris 1-Endangered White sturgeon Acipenser transmontanus 2-Vulnerable Siphatales crassicauda 0-Extinct Cow Head tui chub Siphatales thalassinus vaccaceps 2-Vulnerable High Rock Springs tui chub Siphatales bicolor subspecies 0-Extinct Lahontan lake tui chub Siphatales bicolor pectinifer 2-Vulnerable Owens tui chub Siphatales bicolor snyderi 1-Endangered tui chub Siphatales mohavensis 1-Endangered Bonytail Gila elegans 0-Extinct Arroyo chub Gila orcutti 2-Vulnerable Clear Lake hitch Lavinia exilicauda chi 1-Endangered Monterey hitch Lavinia exilicauda harengeus 2-Vulnerable Red Hills roach Lavinia symmetricus subspecies 2-Vulnerable Northern (Pit) roach Lavinia mitrulus 2-Vulnerable Sacramento splittail Pogonichthys macrolepidotus 2-Vulnerable Clear Lake splittail Pogonichthys ciscoides 0-Extinct Colorado pikeminnow Ptychocheilus lucius 0-Extinct Owens speckled dace Rhinichthys osculus subspecies 1-Endangered Long Valley speckled dace Rhinichthys osculus subspecies 1-Endangered Amargosa Canyon speckled Rhinichthys osculus nevadensis 1-Endangered dace Santa Ana speckled dace Rhinichthys osculus subspecies 1-Endangered Catostomus occidentalis Goose Lake sucker 2-Vulnerable lacusanserinus Modoc sucker Catostomus microps 1-Endangered Klamath largescale sucker Catostomus snyderi 2-Vulnerable Lost River sucker Catostomus luxatus 1-Endangered Santa Ana sucker Catostomus santaanae 1-Endangered Flannelmouth sucker Catostomus latipinnis 1-Endangered Shortnose sucker Chasmistes brevirostris 2-Vulnerable Razorback sucker Xyrauchen texanus 1-Endangered

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Eulachon Thaleichthys pacificus 1-Endangered Longfin smelt Spirinchus thaleichthys 2-Vulnerable Hypomesus pacificus 1-Endangered Bull trout Salvelinus confluentus 0-Extinct Upper Klamath-Trinity fall Oncorhynchus tshawytscha 2-Vulnerable Chinook salmon Upper Klamath-Trinity Oncorhynchus tshawytscha 1-Endangered spring Chinook salmon California Coast fall Chinook Oncorhynchus tshawytscha 2-Vulnerable salmon Central Valley winter Oncorhynchus tshawytscha 2-Vulnerable Chinook salmon Central Valley spring Oncorhynchus tshawytscha 2-Vulnerable Chinook salmon Central Valley late fall Oncorhynchus tshawytscha 1-Endangered Chinook salmon Central Valley fall Chinook Oncorhynchus tshawytscha 2-Vulnerable salmon Central Coast coho salmon Oncorhynchus kisutch 1-Endangered Southern Oregon Northern Oncorhynchus kisutch 1-Endangered California coast coho salmon Pink salmon Oncorhynchus gorbuscha 1-Endangered Chum salmon Oncorhynchus keta 1-Endangered Northern California coast Oncorhynchus mykiss 1-Endangered summer steelhead Klamath Mountains Province Oncorhynchus mykiss 1-Endangered summer steelhead Central California coast Oncorhynchus mykiss 2-Vulnerable winter steelhead Central Valley steelhead Oncorhynchus mykiss 2-Vulnerable South Central California Oncorhynchus mykiss 2-Vulnerable coast steelhead Southern California Oncorhynchus mykiss 1-Endangered steelhead McCloud River redband trout Oncorhynchus mykiss stonei 1-Endangered Eagle Lake rainbow trout Oncorhynchus mykiss aquilarum 2-Vulnerable Kern River rainbow trout Oncorhynchus mykiss gilberti 1-Endangered California golden trout Oncorhynchus mykiss aguabonita 2-Vulnerable Little Kern golden trout Oncorhynchus mykiss whitei 2-Vulnerable Paiute cutthroat trout Oncorhynchus clarki seleneris 1-Endangered Lahontan cutthroat trout Oncorhynchus clarki henshawi 2-Vulnerable Desert pupfish Cyprinodon macularius 1-Endangered Owens pupfish Cyprinodon radiosus 1-Endangered Saratoga Springs pupfish Cyprinodon nevadensis nevadensis 2-Vulnerable Amargosa River pupfish Cyprinodon nevadensis amargosae 2-Vulnerable Tecopa pupfish Cyprinodon nevadensis calidae 0-Extinct Shoshone pupfish Cyprinodon nevadensis shoshone 1-Endangered

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Salt Creek pupfish Cyprinodon salinus salinus 2-Vulnerable Cottonball Marsh pupfish Cyprinodon salinus milleri 2-Vulnerable Bigeye marbled sculpin Cottus klamathensis macrops 2-Vulnerable Unarmored threespine Gasterosteus aculeatus williamsoni 1-Endangered stickleback Shay Creek stickleback Gasterosteus aculeatus subspecies 1-Endangered Sacramento perch Archoplites interruptus 1-Endangered Tidewater goby Eucyclogobius newberryi 2-Vulnerable

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APPENDIX B

LIST OF DAMS EVALUATED

NID Dam Name County River

CA00002 Mendocino 3 Upper Mendocino Mill Creek CA00004 Marie, Lake Napa Trib Tulucay Creek CA00005 Henderson Amador Jackass Creek CA00011 Rector Creek Napa Rector Creek CA00015 Lower Buck Lake Tuolumne Buck Meadow Creek CA00016 Bigelow Lake Tuolumne East Fork Cherry Creek CA00019 Schmidell Lake El Dorado Trib Rubicon River CA00020 Round Lake El Dorado Upper CA00026 McClure Lake Madera Trib East Fork Granite Creek CA00027 Madera Lake Madera CA00029 Whale Rock San Luis Obispo Old Creek CA00030 Benbow Humboldt South Fork CA00031 Eureka Plumas Eureka Creek CA00032 Frenchman Plumas Little Creek CA00035 Oroville Butte CA00036 Thermalito Diversion Butte Feather River CA00037 Antelope Plumas Indian Creek CA00038 Lower Sardine Lake Sierra Sardine Creek CA00039 Grizzly Valley Plumas Big Grizzly Creek CA00043 Del Valle Alameda Arroyo Valley CA00044 Castaic Los Angeles Castaic Creek CA00049 Cedar Springs San Bernardino West Fork Mojave River CA00052 Pyramid Los Angeles CA00067 Chatsworth Los Angeles Trib Los Angeles River CA00068 Dry Canyon Los Angeles Dry Canyon Creek CA00072 Big Pine Creek Inyo Big Pine Creek Lower San Fernando CA00076 Los Angeles San Fernando Creek (Lower Van Norman) CA00084 Tinemaha Inyo Owens River CA00088 Bouquet Canyon Los Angeles Bouquet Creek CA00089 Grant Lake Mono Rush Creek CA00090 Long Valley Mono Owens River CA00091 Walker Lake Mono Walker Creek CA00092 Sardine Lake Mono Walker Creek

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CA00098 Pleasant Valley Inyo Owens River CA00102 Milliken Napa Milliken Creek CA00104 Conn Creek Napa Conn Creek CA00106 Barrett San Diego Cottonwood Creek CA00108 Hodges, Lake San Diego San Dieguito River CA00109 Savage San Diego Otay River CA00110 Morena San Diego Cottonwood Creek CA00111 El Capitan San Diego San Diego River CA00112 Upper Otay San Diego Val Creek CA00113 San Vicente San Diego San Vicente Creek CA00114 Sutherland San Diego Santa Ysabel Creek CA00120 Early Intake Tuolumne CA00121 Lake Eleanor Tuolumne Eleanor Creek CA00122 Moccasin Lower Tuolumne Moccasin Creek O'Shaughnessy (Hetch CA00123 Tuolumne Tuolumne River Hetchy Reservoir) CA00124 Priest Tuolumne Rattlesnake Creek CA00125 Cherry Valley Tuolumne Cherry Creek CA00126 Calaveras Alameda Calaveras Creek CA00127 Lower Crystal Springs San Mateo San Mateo Creek CA00128 Pilarcitos San Mateo Pilarcitos Creek CA00129 San Andreas San Mateo Trib San Mateo Creek James H Turner (San CA00132 Alameda San Antonio Creek Antonio Reservoir) CA00138 Gibraltar Santa Barbara Santa Ynez River CA00140 Lake Curry Napa Gordon Valley Creek CA00142 Lake Frey Solano Wild Horse Creek CA00149 Napa Bell Creek CA00155 Municipal Solano Trib Suisun Creek CA00156 Newell Santa Cruz San Lorenzo River CA00158 Cherry Flat Santa Clara Penitencia Creek Lake Anza (C L Tilden CA00161 Contra Costa Wildcat Creek Park) Jackson Creek Spillway CA00164 Amador Mokelumne River (Pardee) CA00165 Chabot Alameda CA00166 San Pablo Contra Costa CA00173 Camanche Main San Joaquin Mokelumne River CA00187 Big Dalton Los Angeles Big Dalton Wash CA00188 Big Santa Anita Los Angeles Trib Rio Hondo CA00189 Devils Gate Los Angeles Arroyo Seco CA00190 Cogswell Los Angeles West Fork San Gabriel River CA00191 Big Tujunga No. 1 Los Angeles Big Tujunga Creek CA00192 Live Oak Los Angeles Live Oak Creek

112

CA00193 Pacoima Los Angeles Pacoima Creek CA00194 Puddingstone Los Angeles Walnut Creek CA00195 San Dimas Los Angeles San Dimas Creek CA00196 Sawpit Los Angeles Sawpit Creek CA00198 Thompson Creek Los Angeles Thompson Creek CA00199 Puddingstone Diversion Los Angeles San Dimas Creek CA00200 San Gabriel Los Angeles San Gabriel River CA00204 Alpine Marin Lagunitas Creek CA00205 Lagunitas Marin Lagunitas Creek CA00206 Phoenix Lake Marin Creek CA00207 Bon Tempe Marin Lagunitas Creek CA00208 Peters Marin Lagunitas Creek CA00209 Seeger Marin Nicasio Creek CA00211 Juncal Santa Barbara Santa Ynez River CA00212 Mathews Riverside Trib Cajalco Creek CA00214 Copper Basin San Bernardino Copper Basin CA00216 Morris Los Angeles San Gabriel River CA00223 Robert A Skinner Riverside Tucalota Creek CA00224 Lake Gregory San Bernardino Houston Creek CA00226 Anderson Cottonwood Shasta Sacramento River CA00227 Camp Far West Yuba Bear River CA00228 Weber El Dorado North Fork Webber Creek CA00232 Jacobs Creek El Dorado Jacobs Creek CA00233 Big Sage Modoc Rattlesnake Creek CA00234 Cuyamaca San Diego Boulder Creek CA00237 Littlerock Los Angeles Littlerock Creek Crocker Diversion CA00239 Merced (Snelling Diversion) New Exchequer (Lake CA00240 Mariposa Merced River McClure) CA00242 McSwain Mariposa Merced River CA00243 Modesto Res Stanislaus Trib Tuolumne River Dwinnell Dam (Shasta CA00244 Siskiyou Shasta River River Dam) CA00245 Bowman Nevada Canyon Creek Diversion CA00246 Nevada Deer Creek (Lower Scotts Flat) CA00247 French Lake Nevada Canyon Creek CA00248 Milton Nevada/Sierra Middle CA00249 Lake Combie Nevada Bear River CA00250 Sawmill Main Nevada Canyon Creek CA00252 Jackson Lake Nevada Jackson Creek CA00253 Scotts Flat Nevada Deer Creek

113

CA00254 Jackson Meadows Nevada Middle Fork Yuba River CA00255 Rollins Nevada Bear River CA00256 Faucherie Lake Main Nevada Canyon Creek CA00257 Dutch Flat Afterbay Nevada/Placer Bear River CA00260 Goodwin Calaveras Stanislaus River CA00262 Rodden Lake Stanislaus Lesnini Creek CA00263 Beardsley Tuolumne Middle Fork Stanislaus River CA00264 Donnells Tuolumne Middle Fork Stanislaus River CA00265 Tulloch Calaveras Stanislaus River CA00266 Beardsley Afterbay Tuolumne Middle Fork Stanislaus River CA00267 Wyandotte, Lake Butte North Honcut Creek CA00268 Lost Creek Butte Lost Creek CA00269 Little Grass Valley Plumas CA00270 South Fork Diversion Plumas South Fork Feather River CA00271 Slate Creek Plumas Slate Creek CA00272 Sly Creek Butte Lost Creek CA00273 Forbestown Diversion Butte South Fork Feather River CA00274 Ponderosa Butte South Fork Feather River CA00276 Woodward Stanislaus Simmons Creek CA00277 Concow Butte Concow Creek CA00278 La Grange Stanislaus Tuolumne River CA00281 Don Pedro Main Tuolumne Tuolumne River CA00283 Henshaw San Diego San Luis Rey River CA00284 Bridgeport Mono East Walker Rv CA00285 Woodbridge Div San Joaquin Mokelumne River CA00287 Coyote Santa Clara Coyote Creek CA00288 Calero Santa Clara Calero Creek CA00289 Almaden Santa Clara Almitos Creek CA00290 Guadalupe Santa Clara Guadalupe Creek CA00291 Vasona Percolating Santa Clara Los Gatos Creek CA00292 Stevens Creek Santa Clara Stevens Creek James J. Lenihan CA00293 Santa Clara Los Gatos Creek (Lexington) CA00294 Anderson Santa Clara Coyote River CA00296 Magalia Butte Little Butte Creek CA00297 Paradise Butte Little Butte Creek CA00298 Orange Santiago Creek CA00299 North Fork (Pacheco Dam) Santa Clara Pacheco Creek CA00300 West Valley Modoc West Valley Creek CA00301 Peoples Weir Kings Kings River CA00303 Island Weir Kings North Fork Kings River CA00304 Fairmount Park Riverside Trib CA00305 Mockingbird Canyon Riverside Mockingbird Canyon

114

CA00306 Redhawk Lake Calaveras Rich Gulch CA00307 Middle Fork Diversion Tulare Middle Fork CA00310 Kimball Creek Napa Kimball Creek CA00312 Matilija Ventura Matilija Creek CA00313 Runkle Ventura Runkle Canyon CA00321 Novato Creek Marin Novato Creek CA00323 Copco No 1 Siskiyou Klamath River CA00325 Iron Gate Siskiyou Klamath River CA00326 Butt Valley Plumas Butt Creek CA00327 Lake Almanor Plumas CA00328 Poe Butte North Fork Feather River CA00329 Cresta Plumas North Fork Feather River CA00330 Rock Creek Plumas North Fork Feather River Lower Bucks Lake (Bucks CA00331 Plumas Bucks Creek Diversion) Bucks Lake (Bucks CA00332 Plumas Bucks Creek Storage) CA00333 Grizzly Forebay Plumas Grizzly Creek CA00334 Three Lakes Plumas Milk Ranch Creek CA00335 Balch Diversion Fresno North Fork Kings River CA00336 Balch Afterbay Fresno North Fork Kings River CA00337 Crane Valley (Bass Lake) Madera North Fork Willow Creek CA00340 Kerckhoff Madera San Joaquin River CA00341 Merced Falls Merced Merced River Manzanita Lake CA00342 Madera North Fork Willow Creek (Manzanita Diversion) Trib West Branch Feather CA00344 Kunkle Butte River CA00345 Philbrook Butte Philbrook Creek CA00346 Round Valley Butte West Branch Feather River CA00351 Fuller Lake Nevada Jordan Creek CA00356 Lake Arthur Placer South Fork Dry Creek CA00357 Lake Fordyce Nevada Fordyce Creek CA00358 Lake Spaulding Nevada South Fork Yuba River CA00359 Lake Sterling Nevada Trib Fordyce Creek Trib North Fork American CA00361 Lake Valley Main Placer River CA00363 Lower Feeley (Carr Lake) Nevada Trib Fall Creek CA00364 Lower Lindsey Nevada Trib Texas Creek Lower Peak Lake CA00365 Placer Trib South Fork Tuba River (Cascade Lakes) CA00366 Meadow Lake Nevada Trib Fordyce Creek CA00367 Middle Lindsey Nevada Trib Texas Creek CA00368 Rock Creek Main Placer Rock Creek

115

CA00369 Rucker Lake Nevada Rucker Creek CA00370 Upper Feeley Lake Nevada Trib Fall Creek Upper Peak Lake CA00371 Placer Trib South Fork Yuba River (Cascade Lakes) CA00373 White Rock Lake Nevada Trib North Creek CA00374 Echo Lake El Dorado Echo Creek Medley Lakes Main (Lake Trib South Fork American CA00376 El Dorado Aloha) River CA00377 Silver Lake Amador Silver Fork CA00378 Caples Lake (Twin Lake) Alpine Trib Silver Fork CA00379 Upper Bear Amador Bear River CA00380 Lower Blue Lake Alpine Blue Creek CA00381 Meadow Lake Alpine Trib North Fork Mokelumne CA00382 Salt Springs Amador North Fork Mokelumne River CA00384 Twin Lakes Alpine Trib North Fork Mokelumne CA00385 Upper Blue Lake Alpine Blue Creek CA00387 Lyons Tuolumne South Fork Stanislaus River CA00388 Strawberry (Pinecrest) Tuolumne South Fork Stanislaus River CA00389 Phoenix Tuolumne Sullivan Creek CA00390 Relief Tuolumne Summit Creek CA00393 Macumber Shasta North Fork Battle Creek CA00394 North Battle Creek Shasta North Fork Battle Creek Pit No. 3 Diversion CA00395 Shasta Pit River (Britton Lake) CA00397 Pit No. 4 Diversion Shasta Pit River CA00398 Scott Lake Eel River Cape Horn Dam (Van CA00399 Mendocino South Eel River Arsdale Reservoir) CA00400 Tiger Creek Regulator Amador Tiger Creek CA00401 Tiger Creek Afterbay Amador North Fork Mokelumne River CA00402 Pit No. 5 Diversion Shasta Pit River Hat Creek No. 2 Diversion CA00404 Shasta Hat Creek (Baum Lake) CA00405 Pit No. 1 Forebay Shasta Fall River CA00406 Morris Mendocino James Creek CA00407 Indian Ole Lassen Hamilton Creek CA00409 Lower Bear Amador Bear River CA00411 Wishon Main Fresno North Fork Kings River CA00412 Courtright Fresno Helms Creek Belden Forebay (Caribou CA00413 Plumas North Fork Feather River Afterbay) CA00414 Pit No. 6 Diversion Shasta Pit River CA00415 Pit No. 7 Diversion Shasta Pit River CA00416 McCloud Diversion Shasta McCloud River CA00417 Iron Canyon Shasta Iron Canyon Creek

116

CA00418 Chili Bar El Dorado South Fork American River CA00421 New Drum Afterbay Nevada Bear River CA00422 Alpine Main Alpine Silver Creek CA00423 Hunters Calaveras Mill Creek CA00424 Ross Calaveras French Gulch Creek CA00426 Union Main Alpine North Fork Stanislaus River CA00427 Utica Main Alpine North Fork Stanislaus River CA00432 Big Creek Dam No. 6 Fresno San Joaquin River CA00433 Florence Lake Fresno South Fork San Joaquin River Big Creek Dam No. 3a CA00434 Fresno Big Creek (Huntington) CA00435 Lady Franklin Lake Tulare CA00437 Shaver Lake Fresno Stevenson Creek Big Creek Dam No. 7 CA00440 Fresno San Joaquin River (Redinger Lake) CA00441 Vermilion (Edison) Fresno Mono Creek CA00442 Portal Forebay Main Fresno Trib South Fork San Joaquin CA00443 Mammoth Pool Fresno San Joaquin River CA00446 Hillside Inyo South Fork Bishop Creek CA00447 Longley Inyo McGee Creek CA00448 Sabrina Inyo Middle Fork Bishop Creek CA00450 Rush Creek Meadows Mono Rush Creek CA00451 Lundy Lake Mono Mill Creek CA00454 Agnew Lake Mono Rush Creek CA00455 Saddlebag Mono Lee Vining Creek CA00456 Tioga Lake Mono Glacier Creek CA00457 Rhinedollar (Ellery Lake) Mono Lee Vining Creek CA00459 McBrien Modoc Pit River CA00461 SX (Essex) Modoc Trib Pit River CA00462 Huffman Antelope Modoc Clover Swale Taylor (Taylor Creek No. CA00463 Modoc Taylor Creek 1) CA00464 Janes Flat Modoc Mosquito Creek CA00465 Davis Creek Orchard Modoc Roberts Creek CA00466 Capik Modoc Trib North Fork Pit River Big Dobe North (Baker CA00467 Modoc Trib Rattlesnake Creek and Thomas Reservoir) Big Dobe South (Baker CA00468 Modoc Trib Rattlesnake Creek and Thomas Reservoir) CA00471 Little Juniper Modoc Little Juniper Creek CA00472 Graven Modoc Trib Canyon Creek CA00473 Plum Canyon Modoc Plum Creek Ingals Swamp (Dorris CA00474 Modoc Ingals Swamp Brothers Reservoir)

117

CA00475 Payne Modoc Trib South Fork Pit River CA00480 Duncan Creek Diversion Modoc Trib Pit River CA00481 Rye Grass Swale Modoc Trib Canyon Creek CA00482 White Modoc Trib Pit River CA00483 Toreson Modoc Toms Creek CA00484 Kramer Modoc Widow Valley Creek CA00485 Roberts Modoc Trib Pit River CA00486 Enquist Modoc Trib Olivers Can CA00487 Danhauser Modoc Trib South Fork Pit River CA00488 Upper Pasture Modoc Yankee Jim Slough CA00489 Lookout Modoc Pit River CA00491 Carpenter Wilson Modoc Cooley Gulch CA00492 Leonard Johnson Modoc Dry Creek CA00494 Donovan Modoc Rye Grass Swale CA00495 Campbell Lake Siskiyou Shackleford Creek CA00496 Ray Soule Reservoir Siskiyou Trib Little Shasta River CA00509 Round Valley Lassen Round Val Cr CA00510 Red Rock No 1 Lassen Red Rock Creek CA00512 Silva Flat Lassen Juniper Creek CA00513 Coyote Flat Lassen Coyote Creek CA00514 Caribou Lake Lassen Susan River CA00515 Hog Flat Lassen Tr Susan River CA00516 Leavitt, Lake Lassen Tr Susan River CA00517 McCoy Flat Lassen Susan River CA00519 Buckhorn Lassen Buckhorn Creek CA00522 Coon Camp Lassen Tr Horse Lake CA00524 Branham Flat Lassen Branham Creek CA00525 Heath Reservoir Lassen Slate Creek CA00528 Rye Tehama Kendrick Creek CA00530 Bidwell Lake Plumas North Canyon Creek CA00531 Silver Lake Plumas Silver Creek CA00532 Grizzly Creek Plumas Big Grizzly Creek CA00533 Taylor Lake Plumas Trib Indian Creek CA00534 Long Lake Plumas Gray Eagle Creek CA00535 Palen Sierra Antelope Creek CA00537 Donner Lake Nevada Donner Creek CA00538 Lake Vera Nevada Rock Creek CA00541 Pine Grove Nevada Little Shady Creek CA00542 Bellett Nevada Trib Shady Creek CA00546 Morning Star Res Placer North Forbes Creek CA00548 Los Verjels Yuba Dry Creek CA00551 Cannon Ranch Butte Trib Oregon Gulch CA00554 York Hill Colusa Trib Bear Creek

118

CA00555 Rancho Rubini Colusa Trib Bear Creek CA00556 E A Wright Glenn Small Creek CA00558 Hamilton Glenn Trib Watson Creek CA00560 Ridgewood Mendocino Forsythe Creek CA00561 McNab Mendocino McNab Creek CA00562 Bevans Creek Mendocino Bevans Creek CA00563 Scout Trib Berry Creek Geunoc Lake (Detert CA00564 Lake Bucksnort Creek Lake) CA00565 McCreary Lake Bucksnort Creek CA00566 Bordeaux, Lake Lake Trib Bucksnort Creek CA00571 Spring Valley Lake Wolf Creek CA00572 Coyote Creek Lake Coyote Creek CA00574 Catacoula Napa Maxwell Creek CA00578 Henne Napa Angwin Branch CA00581 Duvall Napa Trib Pope Creek CA00583 Moskowite Napa Trib Capell Creek CA00585 Dick Week Napa Trib Pope Creek CA00586 William, Lake Napa Trib Milliken Creek CA00591 Mallacomes Sonoma Foote Creek CA00597 Lake Solano Dug Road Gulch CA00601 Blodgett Sacramento Laguna Creek CA00602 Van Vleck Sacramento Trib Arkansas Creek CA00605 Hamel Sacramento Trib Dry Creek CA00607 Mark Edson El Dorado Pilot Creek CA00608 Williamson No 1 El Dorado Trib Weber Creek CA00610 D Agostini El Dorado Spanish Creek CA00611 Big Canyon Creek El Dorado Big Canyon Creek CA00612 Goffinet Amador Jackass Creek CA00615 John Orr Amador Trib Jackson Creek CA00617 Shenandoah Lake Amador Pigeon Creek CA00618 Emery Calaveras McKinney Creek CA00619 Bevanda Calaveras Trib CA00620 Salt Springs Valley Calaveras Rock Creek CA00621 McCarty Calaveras Trib Johnny Creek CA00622 Mountain King Calaveras Clover Creek CA00624 FlyInAcres Calaveras Moran Creek CA00627 Flowers Calaveras Little Johns Creek CA00628 Cherokee Calaveras Cherokee Creek CA00629 Scott Lake Alpine Tr Wfk Carson R CA00630 Crater Lake Alpine Crater Lake Creek CA00631 Red Lake Alpine Red Lake Creek

119

CA00634 Kinney Meadows Alpine Tr Silver Creek CA00635 Lower Kinney Lake Alpine Tr Silver Creek CA00641 Heenan Lake Alpine Tr Efk Carson R CA00643 Upper Twin Lake Mono Robinson Creek CA00644 Lower Twin Lake Mono Robinson Creek CA00646 Black Reservoir Mono Black Creek CA00648 Poore Lake Reservoir Mono Poore Creek CA00649 Twain Harte Tuolumne Trib Sullivan Creek CA00652 Big Creek Tuolumne Big Creek CA00653 Tuolumne Log Pond Tuolumne Turn Back Creek CA00654 Orvis Stanislaus Buckham Gulch CA00655 Gilmore San Joaquin Trib Mormon Slough CA00656 Davis No 2 San Joaquin Trib Calaveras River CA00657 Foothill Ranch San Joaquin Trib Calaveras River CA00664 Lucerne, Lake San Mateo Arroyo De Los Frijoles Bean Hollow #2 (De Los CA00665 San Mateo Arroyo De Los Frijoles Frijoles) Bean Hollow #3 (De Los CA00666 San Mateo Arroyo De Los Frijoles Frijoles) CA00669 Searsville San Mateo Corte Madera Creek CA00674 Notre Dame San Mateo Belmont Creek CA00675 Grant Company 2 Santa Clara Arroyo Aguague CA00676 Lake Ranch Santa Clara Beardsley Creek CA00679 Williams Santa Clara Los Gatos Creek CA00680 Austrian Santa Clara Los Gatos Creek CA00688 Mill Creek Santa Cruz Mill Creek CA00689 San Clemente Monterey Carmel River CA00692 Los Padres Monterey Carmel River CA00694 Hawkins San Benito Trib Arroyo De Las Viboras CA00698 Kelsey Merced Trib South Fork Dry Creek CA00699 Stockton Creek Mariposa Stockton Creek CA00700 Green Valley Mariposa Smith Creek CA00701 McMahon Mariposa Maxwell Creek CA00702 Hendricks Head Diversion Butte Trib Horse Creek CA00705 Sierra Vista Madera CA00706 Jane, Lake Madera Trib Hildreth Creek CA00707 Black Hawk Madera Coarse Creek CA00708 Spring Madera Longhollow Creek CA00709 Sequoia Lake Fresno Mill Flat Creek CA00713 Empire Weir No 2 Kings CA00719 Rancho Del Ciervo Santa Barbara Trib San Jose Creek CA00724 Los Tablas Creek San Luis Obispo Las Tablas Creek CA00725 Righetti San Luis Obispo West Corral De Pie

120

CA00726 San Marcos San Luis Obispo San Marcos Creek CA00727 Hartzell San Luis Obispo Santa Rita Creek CA00729 Tejon Storage 2 Kern Trib Tejon Creek CA00731 Alisal Creek Santa Barbara Alisal Creek CA00736 Lake Sherwood Ventura Potrero Valley Creek CA00737 Eleanor, Lake Ventura Eleanor Creek CA00739 Malibu Lake Club Los Angeles Malibu Creek CA00742 Lindero Los Angeles Lindero Creek CA00743 Potrero Los Angeles Potrero Valley CA00745 Orange Trib Newport Bay CA00746 Peters Canyon Orange Peters Canyon CA00747 Bonita Canyon Orange CA00748 Laguna Orange Trib CA00750 Veeh Orange Trib San Diego Creek CA00755 Chino Ranch #1 San Bernardino Tonner Canyon Creek CA00757 Bear Valley San Bernardino Bear Creek CA00758 Green Val Lake San Bernardino Green Valley Creek CA00759 Lake Arrowhead San Bernardino Little Bear Creek CA00760 Grass Valley San Bernardino Grass Valley Creek CA00761 Rancho Cielito San Bernardino Trib Chino Creek CA00763 Lake Hemet Riverside Trib San Jacinto River CA00764 Little Lake Riverside Trib San Jacinto CA00765 Railroad Canyon Riverside San Jacinto River CA00766 Lee Lake Riverside Temescal Creek CA00770 Vail Riverside Temecula Creek CA00771 Quail Valley Riverside Trib San Jancinto River CA00772 Wohlford Lake San Diego Escondido Creek CA00774 Corte Madera San Diego Trib Pine Valley CA00775 Sweetwater Main San Diego Sweetwater River CA00776 Lake Loveland San Diego Sweetwater River CA00777 Jr San Diego Skye Valley CA00780 Wuest San Diego Mc Cain Creek CA00781 Calavera San Diego Calavera Creek CA00782 San Marcos San Diego San Marcos Creek CA00786 Thing Valley San Diego La Posta Creek CA00789 Palo Verde San Diego Sweetwater River CA00791 Healdsburg Recreation Sonoma Russian River CA00794 Matanzas Creek Sonoma Matanzas Creek CA00796 Woodcrest Riverside Woodcrest Creek CA00797 Harrison Street Riverside Harrison Creek CA00798 Alessandro Riverside Alessandro Creek CA00799 Prenda Riverside Prenda Creek

121

CA00800 Sycamore Riverside Sycamore Canyon CA00801 Pigeon Pass Riverside Pigeon Pass CA00802 Boxsprings Riverside Box Springs Creek CA00804 Lake Madrone Butte Berry Creek CA00805 Santa Felicia Ventura Piru Creek CA00806 Elmer J Chesbro Santa Clara Llagas Creek CA00807 Uvas Santa Clara Uvas Creek CA00808 Pine Creek Contra Costa Pine Creek CA00809 Marsh Creek Contra Costa Marsh Creek CA00810 Deer Creek Contra Costa Deer Creek CA00811 Dry Creek Contra Costa Dry Creek CA00812 Nacimiento San Luis Obispo Nacimiento River CA00813 San Antonio Monterey San Antonio River CA00814 Ice House Main El Dorado South Fork Silver Creek CA00815 Junction El Dorado Silver Creek CA00816 Union Valley El Dorado Silver Creek CA00817 Camino El Dorado Silver Creek CA00818 Gerle Creek El Dorado Gerle Creek CA00820 Loon Lake Main El Dorado Gerle Creek CA00821 Buck Island Main El Dorado Little Rubicon CA00822 Rubicon Main El Dorado Rubicon River CA00823 Slab Creek El Dorado South Fork American River CA00824 Brush Creek El Dorado Brush Creek CA00825 Rancho Seco Sacramento Trib Hadselville Creek CA00827 Adobe Creek Lake Adobe Creek CA00828 Highland Creek Lake Highland Creek CA00829 Villa Park Orange Santiago Creek Ruth Lake (R. W. CA00833 Trinity Mad River Matthews) CA00835 Berenda Slough Madera Berenda Slough CA00837 Redbank Fresno Redbank Creek CA00839 Ward Creek Alameda Ward Creek CA00840 Cull Creek Alameda Cull Creek San Lorenzo Creek (Don CA00841 Alameda San Lorenzo Creek Castro) CA00842 Virginia Ranch Yuba Dry Creek CA00845 Copperopolis Calaveras Penney Creek CA00847 Paicines San Benito Trib Tres Pinos Creek CA00848 Hernandez San Benito San Benito River CA00849 Russian River No 1 Sonoma Russian River CA00850 Wood Ranch Ventura Trib Arroyo Simi CA00851 Herman, Lake Solano Sulphur Springs Creek CA00854 Sand Canyon Orange Sand Canyon

122

L. L. Anderson (French CA00856 Placer Middle Fork American River Meadows) CA00857 Hell Hole Placer Rubicon River CA00858 Middle Fork Interbay Placer Middle Fork American River CA00859 Ralston Afterbay Placer Middle Fork American River CA00863 New Bullards Bar Yuba North Yuba River CA00864 Our House Sierra Middle Fork Yuba River CA00865 Log Cabin Yuba Oregon Creek CA00866 Francis, Lake Yuba Dobbins Creek CA00867 Jackson Creek Amador Jackson Creek CA00871 Ada Rose, Lake Mendocino Trib Willets Creek Emily (Brooktrails 3 CA00872 Mendocino Willits Creek North) CA00873 Sulphur Creek Orange Sulphur Creek CA00874 Maine Prairie 3 Solano Ulatis Creek CA00878 Dixon San Diego Trib Escondido Creek Mendota Diversion CA00886 Fresno San Joaquin River (Mendota Pool) CA00887 Lopez San Luis Obispo Arroyo Grande Creek CA00888 Terminal San Luis Obispo Trib Arroyo Grande CA00889 Box Canyon Siskiyou Sacramento River CA00904 Westlake Reservoir Los Angeles Tree Springs Creek CA00905 Turner San Diego Moosa Canyon CA00906 San Dieguito San Diego Trib Escondido Creek CA00909 Poway San Diego Warren Canyon CA00910 Holiday Lake El Dorado Sawmill Creek CA00911 Cache Creek (Clear Lake) Lake Cache Creek CA00914 Lindauer Concrete Modoc Pit River CA00915 A And C (Avenzino Res) Modoc South Fork Willow Creek CA00916 Poison Springs Modoc Rock Creek CA00920 Bayley Res Modoc Crooks Canyon CA00921 Renner Sibley Cr Modoc Sibley Creek CA00922 Boggs And Warren Modoc East Sand Creek CA00925 James Modoc Trib Parker Creek CA00926 Shelley Siskiyou Webb Gulch CA00929 Dwight Hammond Siskiyou Trib Shasta River CA00933 Null Shasta Rock Creek CA00934 Ross No 1 Shasta Trib Stillwater Creek CA00938 Peconom Lassen Antelope Val CA00940 Cramer Lassen Tr Horse Lake CA00941 Gerig Lassen Pit River CA00942 Mendiboure Lassen Tr Van Loan Cr CA00944 Smoke Creek (W) Lassen Smoke Creek

123

CA00945 Holbrook Lassen Ash Creek CA00946 Iverson Lassen Trib Juniper Creek CA00947 Elkins And Lane Lassen Trib Ash Creek CA00948 Albaugh No 1 Lassen Trib Pit River CA00949 Albaugh No 2 Lassen Trib Willow Creek CA00952 Spaulding Lassen Tr Madelin Plains CA00953 Myers Lassen Trib Ash Creek CA00954 Madeline Lassen Tr Madeline Plains CA00956 Tule Lake (Moon Lake) Lassen Cedar Creek CA00957 Spooner Lassen Trib Ash Creek CA00960 Leonard No 2 Lassen Trib Ash Creek CA00961 Petes Valley Lassen Petes Creek CA00964 Anthony House Nevada Deer Creek CA00965 Swan Nevada Dry Creek CA00966 Magnolia Nevada Magnolia Creek CA00969 Lakewood Placer Dry Creek CA00971 Ice Lakes Placer Serena Creek CA00973 Williams Valley Mendocino Trib Short Creek CA00974 Round Mountain Mendocino Trib York Creek CA00976 McGuire Mendocino South Fork Noyo River CA00979 Olsen Shasta Ledgewood Creek CA00997 Indian Creek El Dorado Indian Creek CA00998 Barnett El Dorado Barnett Creek CA01001 Volo Mining Company El Dorado Indian Creek CA01002 Tanner Calaveras Cowell Creek CA01005 White Pines Calaveras San Antonio Creek CA01008 Pomponio Ranch San Mateo Pomponio Creek CA01010 Green Oaks #1 San Mateo Green Oaks Creek CA01011 Coit Santa Clara Trib North Fork Pacheco Creek CA01013 Murry Santa Clara Mississippi Creek CA01015 R Simoni Irrigation Santa Clara Hay Canyon CA01016 Laurel Springs Club Santa Clara Middle Fork Coyote Creek CA01027 Misselbeck Shasta North Fork Cottonwood CA01028 Truett Shasta Ash Creek CA01029 Nash Shasta Trib Stillwater Creek CA01030 Haynes Res Shasta Goose Creek CA01045 Schubin El Dorado Trib Webber Creek CA01046 Manhattan Creek El Dorado Manhattan Creek CA01048 Aeree El Dorado Trib Pilot Creek CA01050 Patterson El Dorado Deadman Creek Thurman (Hawkeye CA01052 Shasta Slaughter Pole Ranch) CA01055 Eaton H. Magoon Lake Napa Routan Creek

124

(Upper Bohn Lake) CA01059 Budge Sonoma Trib Russian River CA01062 Pinheiro Sonoma Trib CA01064 Straza El Dorado Black Rock Creek CA01065 Abrams El Dorado Hastings Creek CA01067 Hillside Ranch Sonoma Trib House Creek CA01075 Big Dry Creek Fresno Big Dry Cr & Do CA01076 Chorro Creek San Luis Obispo Chorro Creek CA01082 New U San Leandro Alameda San Leandro Creek CA01083 Soulajule Marin Arroyo Sausal CA01086 Camp Far West Diversion Yuba Bear River CA01088 Cloverswale Modoc Trib Witcher Creek CA01097 Mustang Creek Merced Mustang Creek CA01098 Bravo Lake Reservoir Tulare Wutchumna Ditch CA01101 Eagle Ranch San Luis Obispo Creek CA01107 Indian Valley Lake North Fork Cache Creek CA01115 Top Cat Tehama Trib Brannin Creek CA01116 Sunflower Tehama Sunflower Gulch CA01119 Clementia Sacramento Trib CA01122 Mission Viejo, Lake Orange CA01123 Trampas Canyon Orange Trampas Canyon CA01131 Yucaipa No 1 San Bernardino Trib Yucaipa Creek CA01132 Yucaipa No 2 San Bernardino Trib Yucaipa Creek CA01145 Upper Oso Orange Oso Creek CA01158 Sierra Madre Villa Los Angeles Sierra Madre Canyon CA01179 Oak Street Riverside Oak Street Creek CA01180 Sand Creek Tulare Sand Creek CA01199 Cameron Park El Dorado Deer Creek CA01205 Homestake Tailings Lake Trib Hunting Creek CA01208 Halls Meadows Modoc Couch Creek CA01211 Mary Street Riverside Alessandro Wash CA01213 Antelope Kern Antelope Creek CA01215 Ramona San Diego Green Val Road Creek CA01216 Steidlmayer #3 Sutter Unnamed CA01217 Las Llajas Ventura Las Llajas Can CA01223 Davis Creek Yolo Davis Creek CA01224 New Spicer Meadow Tuolumne Highland Creek CA01225 Galt Sacramento Trib Laguna Creek CA01230 Lakeport Lake Trib Manning Creek CA01234 North Fork Diversion Alpine North Fork Stanislaus River CA01238 Isabel Lake No 1 Santa Clara Trib CA01240 Edwards Reservoir Santa Barbara Trib Gato Creek

125

CA01246 Centennial Mendocino Davis Creek CA01248 Dove Canyon Orange Dove Creek CA01250 Smiths Reservoir Merced Trib Burns Creek CA01251 Rubber Dam 3 Alameda Alameda Creek CA01252 Pine Creek Detention Contra Costa Pine Creek CA01255 Isabel Lake No 2 Santa Clara Trib Isabel Creek CA01257 McKays Point Diversion Calaveras North Fork Stanislaus River CA01262 Jayne s Lake Mendocino Toney Creek CA01263 Bradford Mendocino Trib Russian River CA01265 Bottoms Lake Trib Helena Creek CA01266 Sycamore Canyon Ventura Sycamore Can CA01270 California Park Butte Dead Horse Slough CA01289 Metcalf Napa Trib Maxwell Creek CA01303 Flotation Tails Calaveras Trib Littlejohns Creek CA01306 Middle Cooperstown Tuolumne Trib Dry Creek CA01307 Kilmer Tuolumne Trib Dry Creek CA01309 Shaffer El Dorado Indian Creek CA01313 Merlo Sonoma Fall Creek CA01314 Calaveras Trib Bear Creek Lagoon Valley County CA01315 Solano Trib Laguna Creek Park CA01327 Fancher Creek Fresno Fancher Cr & Hog Creek CA01335 Golden Rule Mendocino Trib Walker Creek CA01351 Rubber Dam 1 Alameda Alameda Creek CA01355 Castle Merced Canal Creek CA01361 Agua Chinon Orange Agua Chinon Wash CA01380 Rubber Dam 2 Alameda Alameda Creek CA01406 Amargosa Creek Los Angeles Amargosa Creek SVCSD Reclamation Pond CA01408 Mendocino Trib Mcdowell Creek 2 (Hooper No. 2) CA01412 Arundell Barranca Ventura Arundell Barranca CA01423 Lolonis Vineyards Mendocino Trib West Fork Russian River CA01425 Jack s Swamp Dam No 2 Modoc Trib Pit River CA01428 Skyrocket Calaveras Littlejohn Creek Unnamed Tributary To CA01450 Upper Wilcox Madera Picayunne Creek CA10019 Hansen Los Angeles Tujunga Wash CA10020 Lopez Los Angeles Pacoima Wash CA10021 Mojave Dam San Bernardino W Fk Mojave River CA10023 San Antonio Dam San Bernardino San Antonio Creek CA10024 Santa Fe Los Angeles San Gabriel River CA10025 Sepulveda Los Angeles Los Angeles River CA10027 Whittier Narrows Dam Los Angeles San Gabriel River CA10101 Bear Mariposa Bear Creek

126

CA10102 Black Butte Tehama Stony Creek CA10103 Burns Merced Burns Creek CA10104 Farmington Dam San Joaquin Rock And Littlejohn Creeks CA10105 Englebright Yuba Yuba River CA10106 Isabella Kern Kern River CA10107 Mariposa Dam Mariposa CA10108 Martis Creek Nevada Martis Creek CA10109 New Hogan Dam Calaveras Calaveras River CA10110 North Fork Placer North Fork American River CA10111 Owens Dam Mariposa Owens Creek CA10112 Pine Flat Fresno Kings River CA10113 Success Tulare CA10114 Terminus (Lake Kaweah) Tulare Kaweah River CA10123 Hughes (Dam #36) Monterey Aqua Fria Creek Santa Margarita River CA10131 Lake Oneill San Diego Offstream CA10134 Antelope Shasta Pit River CA10135 Boca Nevada Little Truckee River CA10136 Bradbury Santa Barbara Santa Ynez River CA10139 Casitas Ventura Coyote Creek CA10141 Clear Lake Modoc Lost River CA10144 Dorris Modoc Stockdill Slough CA10145 East Park Dike No. 1 (N) Colusa Little Stony Creek CA10148 Folsom Sacramento American River CA10154 Friant Fresno San Joaquin River CA10156 Glen Anne Santa Barbara West Fork Glen Annie Canyon CA10159 Imperial Diversion Imperial Colorado River CA10160 Keswick Shasta Sacramento River CA10162 Placer Truckee River CA10163 Lauer Modoc Trib Pit River CA10164 Lauro Santa Barbara Diablo Creek CA10165 Lewiston Trinity Trinity River CA10166 Little Panoche Detention Fresno Little Panoche Creek Los Banos Creek CA10167 Merced Los Banos Creek Detention Dam CA10169 McGinty Modoc Mud Creek CA10170 Monticello Yolo Putah Creek CA10174 Nimbus Sacramento American River CA10179 Prosser Creek Nevada Prosser Creek CA10180 Putah Diversion Yolo, Solano Putah Creek CA10181 Red Bluff Diversion Tehama Sacramento River CA10186 Shasta Shasta Sacramento River CA10187 Sly Park (Jenkinson) El Dorado Sly Park Creek

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CA10192 Stampede Sierra Little Truckee River CA10194 Stony Gorge Glenn Stony Creek CA10196 Trinity Trinity Trinity River CA10197 Twitchell San Luis Obispo Cuyama River CA10201 Coyote Valley Dam Mendocino East Fork Russian River CA10202 Salinas San Luis Obispo Salinas River CA10204 Whiskeytown Shasta Clear Creek CA10207 Emigrant Lake Tuolumne North Fork Cherry Creek CA10210 Telephone Flat Modoc Trib Boles Creek CA10212 Y Meadow Tuolumne Rock Creek CA10213 Walker Mine Tails Plumas Dolly Creek CA10216 Fallen Leaf El Dorado Taylor Creek CA10219 Snow Lake Tuolumne Trib East Fork Cherry Creek CA10220 Middle Emigrant Tuolumne North Fork Cherry Creek CA10221 Upper Buck Lake Tuolumne Buck Meadow Creek CA10222 Long Lake Tuolumne West Fork Cherry Creek CA10224 Herring Creek Tuolumne Herring Creek CA10225 Bear Lake Tuolumne Lily Creek CA10226 Leighton Lake Tuolumne Yellow CA10227 Swains Hole Lassen Butte Creek CA10228 Lower Salmon Lake Sierra Trib Salmon Creek CA10229 U Salmon Lake Sierra Trib Salmon Creek CA10232 Weaver Nevada Eastfork CA10233 Blue Lake Lassen Outlet Creek CA10239 Smith Lake Plumas Wapaunsie Creek CA10243 Buchanan Madera Chowchilla River CA10244 Hidden Dam Madera Fresno River CA10245 Funks Colusa Funks Creek CA10246 New Melones Calaveras Stanislaus River CA10266 Manzanita Lake Shasta Manzanita Creek CA10301 Laguna Imperial Colorado River CA10302 Upper Letts Colusa Letts Creek CA10303 Warm Springs Sonoma Dry Creek CA10305 Parker San Bernardino Colorado River CA10306 Sugar Pine Placer North Shirttail Creek CA10307 Hume Lake Fresno Ten Mile Creek CA10308 Twin Lakes Mono Mammoth Creek CA10313 Everly Modoc Long Branch Cyn CA10318 South Mountain Modoc Trib Fletcher Creek CA10320 Green Tank Modoc Trib Fletcher Creek CA10321 Crowder Mountain Modoc Trib Telephone Flat CA10323 San Justo San Benito Offstream CA10324 Seven Oaks San Bernardino Santa Ana River

128

CA10325 Miners Ravine Detention Modoc Trib Clover Swale Creek CA10326 Boles Meadow Modoc Boles Creek CA10327 Cummings Res No 2 Modoc Pit River Trib CA10329 Grass Lake Plumas Little Jamison Creek CA10330 Jamison Lake Plumas Little Jamison Creek CA10331 Upper Sardine Lake Sierra Trib Sardine Creek CA10336 Bear Valley Lassen Little Davis Creek CA10337 Four Mile Valley No 4 Modoc Fountain Creek CA10339 Emigrant Springs Modoc Null CA10340 East Boulder Siskiyou East Boulder Creek CA10342 Brown Mtn Barrier Los Angeles Arroyo Seco CA10351 Lower Biscar Lassen Snowstorm Creek CA10352 Upper Biscar Lassen Snowstorm Creek CA10354 Nelson Corral Lassen Dry Creek CA20042 Salton Sea Dike Imperial None CA82402 Bayley Modoc Trib Fletcher Creek CA82412 Highland Lake El Dorado Trib Rubicon River Pretty Tree (Emigrant CA82491 Modoc North Fork Pit River Flat Res) CA82501 Wood Flat Modoc North Fork Pit River CA82504 Deer Hill Modoc Trib Fletcher Creek CA82531 Kern No 3 Tulare Kern River CA82904 Rainbow Diversion Colusa Creek CA82938 Buckhorn Trinity Grass Valley Creek CA83069 Chilkoot Madera Chilkoot Creek CA83151 Pit No. 7 Afterbay Shasta Pit River CA83281 Pit River Weir Shasta Pit River CA83283 Bear Creek Div Fresno Bear Creek Schaads Reservoir (CPUD CA83288 Calaveras Middle Fork Mokelumne River Middle Fork)

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APPENDIX C

MODEL PERFORMANCE EVALUATION

Model performance was evaluated by comparing model predictions of mean monthly, maximum 1-day and annual flows at unimpaired, reference gages (Carlisle et al. 2010a) in California with observed flow records. The reference gages used to assess model performance were excluded from the model calibration dataset.

Mean monthly flows, California Inland Mountain Region

January

r-squared 0.947 rmse 119.232 RSR 0.241 Percent bias -2.437 Nash-Sutcliff 0.941 February

r-squared 0.947 rmse 105.658 RSR 0.234 Percent bias -2.526 Nash-Sutcliff 0.945 March

r-squared 0.947 rmse 92.315 RSR 0.231 Percent bias -1.219 Nash-Sutcliff 0.946 April

r-squared 0.950 rmse 92.742 RSR 0.227 Percent bias -2.051 Nash-Sutcliff 0.948 May

r-squared 0.951 rmse 142.362 RSR 0.236 Percent bias -5.568 Nash-Sutcliff 0.944

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June

r-squared 0.971 rmse 115.087 RSR 0.195 Percent bias -5.164 Nash-Sutcliff 0.962 July

r-squared 0.926 rmse 102.356 RSR 0.335 Percent bias -2.381 Nash-Sutcliff 0.886 August

r-squared 0.863 rmse 57.209 RSR 0.371 Percent bias 2.647 Nash-Sutcliff 0.861 September

r-squared 0.896 rmse 38.840 RSR 0.323 Percent bias -2.892 Nash-Sutcliff 0.895 October

r-squared 0.876 rmse 46.340 RSR 0.361 Percent bias -4.408 Nash-Sutcliff 0.868 November

r-squared 0.908 rmse 118.055 RSR 0.322 Percent bias -3.183 Nash-Sutcliff 0.895 December

r-squared 0.942 rmse 123.399 RSR 0.248 Percent bias -1.575 Nash-Sutcliff 0.938

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Annual Maximum 1-day Flow, California Inland Mountain Region r-squared 0.907 rmse 955.224 RSR 0.334 Percent bias -6.282 Nash-Sutcliff 0.887

Annual Mean , California Inland Mountain Region r-squared 0.956 rmse 71.925 RSR 0.230 Percent bias -3.042 Nash-Sutcliff 0.947

Mean monthly flows, California Coastal Mountain Region January

r-squared 0.967 rmse 368.921 RSR 0.187 Percent bias -0.368 Nash-Sutcliff 0.964 February

r-squared 0.978 rmse 292.530 RSR 0.163 Percent bias -3.628 Nash-Sutcliff 0.973 March

r-squared 0.973 rmse 270.338 RSR 0.179 Percent bias -2.595 Nash-Sutcliff 0.967 April

r-squared 0.974 rmse 162.876 RSR 0.161 Percent bias -1.274 Nash-Sutcliff 0.974 May

r-squared 0.916 rmse 209.934 RSR 0.295

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Percent bias 4.033 Nash-Sutcliff 0.911 June

r-squared 0.902 rmse 162.796 RSR 0.318 Percent bias 3.877 Nash-Sutcliff 0.897 July

r-squared 0.901 rmse 110.874 RSR 0.335 Percent bias 10.173 Nash-Sutcliff 0.886 August

r-squared 0.847 rmse 94.363 RSR 0.416 Percent bias 7.247 Nash-Sutcliff 0.824 September

r-squared 0.924 rmse 70.302 RSR 0.284 Percent bias 4.018 Nash-Sutcliff 0.918 October

r-squared 0.979 rmse 93.191 RSR 0.167 Percent bias 2.898 Nash-Sutcliff 0.972 November

r-squared 0.960 rmse 321.465 RSR 0.212 Percent bias -6.312 Nash-Sutcliff 0.954 December

r-squared 0.971 rmse 349.730 RSR 0.181 Percent bias -3.657

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Nash-Sutcliff 0.967 Maximum 1-day Flow, California Coastal Mountain Region r-squared 0.894 rmse 3889.397 RSR 0.327 Percent bias -4.099 Nash-Sutcliff 0.891 Annual Mean , California Coastal Mountain Region r-squared 0.971 rmse 163.390 RSR 0.170 Percent bias -0.729 Nash-Sutcliff 0.971 Mean monthly flows, California Xeric Regions January

r-squared 0.701 rmse 4.550 RSR 0.541 Percent bias 3.511 Nash-Sutcliff 0.701 February

r-squared 0.781 rmse 3.355 RSR 0.466 Percent bias 3.689 Nash-Sutcliff 0.778 March

r-squared 0.779 rmse 3.613 RSR 0.465 Percent bias 2.911 Nash-Sutcliff 0.779 April

r-squared 0.783 rmse 3.689 RSR 0.461 Percent bias 2.570 Nash-Sutcliff 0.783 May

r-squared 0.736 rmse 4.618 RSR 0.512 Percent bias 4.946

134

Nash-Sutcliff 0.732 June

r-squared 0.642 rmse 5.779 RSR 0.593 Percent bias 1.502 Nash-Sutcliff 0.641 July

r-squared 0.474 rmse 8.155 RSR 0.718 Percent bias -0.339 Nash-Sutcliff 0.474 August

r-squared 0.438 rmse 8.946 RSR 0.743 Percent bias -0.612 Nash-Sutcliff 0.437 September

r-squared 9.398 rmse 0.775 RSR -0.496 Percent bias 0.386 Nash-Sutcliff

October 0.410 r-squared 9.419 rmse 0.764 RSR 0.010 Percent bias 0.404 Nash-Sutcliff

November r-squared 0.519 rmse 7.340 RSR 0.688 Percent bias -0.062 Nash-Sutcliff 0.516 December r-squared 0.556 rmse 6.210 RSR 0.660 Percent bias 0.686 Nash-Sutcliff 0.556

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Annual Mean , California Xeric Regions r-squared 0.504 rmse 29.219 RSR 0.699 Percent bias -1.097 Nash-Sutcliff 0.500

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APPENDIX D

LIST OF CANDIDATE DAMS

NID Dam Name County River

CA01361 Agua Chinon Orange Agua Chinon Wash CA00949 Albaugh No 2 Lassen Trib Willow Creek CA00798 Alessandro Riverside Alessandro Creek CA00731 Alisal Creek Santa Barbara Alisal Creek CA00289 Almaden Santa Clara Almitos Creek CA00204 Alpine Marin Lagunitas Creek CA00294 Anderson Santa Clara Coyote River CA00226 Anderson Cottonwood Shasta Sacramento River CA00964 Anthony House Nevada Deer Creek CA00106 Barrett San Diego Cottonwood Creek Bean Hollow #2 (De Los CA00665 San Mateo Arroyo De Los Frijoles Frijoles) CA00757 Bear Valley San Bernardino Bear Creek CA00835 Berenda Slough Madera Berenda Slough Big Dobe North (Baker CA00467 Modoc Trib Rattlesnake Creek and Thomas Reservoir) Big Dobe South (Baker CA00468 Modoc Trib Rattlesnake Creek and Thomas Reservoir) CA01075 Big Dry Creek Fresno Big Dry Cr & Do CA00233 Big Sage Modoc Rattlesnake Creek CA10102 Black Butte Tehama Stony Creek CA10135 Boca Nevada Little Truckee River CA00922 Boggs And Warren Modoc East Sand Creek CA00207 Bon Tempe Marin Lagunitas Creek CA00747 Bonita Canyon Orange Bonita Creek CA00088 Bouquet Canyon Los Angeles Bouquet Creek CA00802 Boxsprings Riverside Box Springs Creek CA10136 Bradbury Santa Barbara Santa Ynez River CA00284 Bridgeport Mono East Walker Rv CA10342 Brown Mtn Barrier Los Angeles Arroyo Seco CA00781 Calavera San Diego Calavera Creek CA00126 Calaveras Alameda Calaveras Creek CA00288 Calero Santa Clara Calero Creek CA10139 Casitas Ventura Coyote Creek

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CA00044 Castaic Los Angeles Castaic Creek CA01355 Castle Merced Canal Creek CA00165 Chabot Alameda San Leandro Creek CA00067 Chatsworth Los Angeles Trib Los Angeles River CA00158 Cherry Flat Santa Clara Penitencia Creek CA01119 Clementia Sacramento Trib Cosumnes River CA01088 Cloverswale Modoc Trib Witcher Creek CA01011 Coit Santa Clara Trib North Fork Pacheco Creek CA00104 Conn Creek Napa Conn Creek CA00214 Copper Basin San Bernardino Copper Basin CA10201 Coyote Valley Dam Mendocino East Fork Russian River Crocker Diversion CA00239 Merced Merced River (Snelling Diversion) CA00840 Cull Creek Alameda Cull Creek CA00487 Danhauser Modoc Trib South Fork Pit River CA00656 Davis No 2 San Joaquin Trib Calaveras River Deer Creek Diversion CA00246 Nevada Deer Creek (Lower Scotts Flat) CA00043 Del Valle Alameda Arroyo Valley CA00537 Donner Lake Nevada Donner Creek CA01248 Dove Canyon Orange Dove Creek CA00068 Dry Canyon Los Angeles Dry Canyon Creek CA00811 Dry Creek Contra Costa Dry Creek Dwinnell Dam (Shasta CA00244 Siskiyou Shasta River River Dam) CA01240 Edwards Reservoir Santa Barbara Trib Gato Creek CA00111 El Capitan San Diego San Diego River CA00806 Elmer J Chesbro Santa Clara Llagas Creek CA10105 Englebright Yuba Yuba River CA00486 Enquist Modoc Trib Olivers Can CA10313 Everly Modoc Long Branch Cyn CA10216 Fallen Leaf El Dorado Taylor Creek CA01327 Fancher Creek Fresno Fancher Cr & Hog Creek CA10104 Farmington Dam San Joaquin Rock And Littlejohn Creeks CA10148 Folsom Sacramento American River CA00657 Foothill Ranch San Joaquin Trib Calaveras River CA00138 Gibraltar Santa Barbara Santa Ynez River CA00655 Gilmore San Joaquin Trib Mormon Slough CA10156 Glen Anne Santa Barbara West Fork Glen Annie Canyon CA00260 Goodwin Calaveras Stanislaus River

138

CA00675 Grant Company 2 Santa Clara Arroyo Aguague CA00089 Grant Lake Mono Rush Creek CA00472 Graven Modoc Trib Canyon Creek CA00290 Guadalupe Santa Clara Guadalupe Creek CA00605 Hamel Sacramento Trib Dry Creek CA10019 Hansen Los Angeles Tujunga Wash CA00797 Harrison Street Riverside Harrison Creek CA00694 Hawkins San Benito Trib Arroyo De Las Viboras CA01030 Haynes Res Shasta Goose Creek CA00525 Heath Reservoir Lassen Slate Creek CA00641 Heenan Lake Alpine Tr Efk Carson R CA00848 Hernandez San Benito San Benito River CA00108 Hodges, Lake San Diego San Dieguito River CA10123 Hughes (Dam #36) Monterey Aqua Fria Creek Ingals Swamp (Dorris CA00474 Modoc Ingals Swamp Brothers Reservoir) CA01255 Isabel Lake No 2 Santa Clara Trib Isabel Creek CA00946 Iverson Lassen Trib Juniper Creek CA01425 Jack s Swamp Dam No 2 Modoc Trib Pit River James H Turner (San CA00132 Alameda San Antonio Creek Antonio Reservoir) CA00706 Jane, Lake Madera Trib Hildreth Creek CA00211 Juncal Santa Barbara Santa Ynez River CA82531 Kern No 3 Tulare Kern River CA10160 Keswick Shasta Sacramento River CA00278 La Grange Stanislaus Tuolumne River CA00748 Laguna Orange Trib San Diego Creek Lake Anza (C L Tilden CA00161 Contra Costa Wildcat Creek Park) CA00759 Lake Arrowhead San Bernardino Little Bear Creek CA00140 Lake Curry Napa Gordon Valley Creek CA00142 Lake Frey Solano Wild Horse Creek CA00224 Lake Gregory San Bernardino Houston Creek CA00763 Lake Hemet Riverside Trib San Jacinto River Santa Margarita River CA10131 Lake Oneill San Diego Offstream CA01230 Lakeport Lake Trib Manning Creek CA00745 Lambert Orange Trib Newport Bay CA01217 Las Llajas Ventura Las Llajas Can CA10164 Lauro Santa Barbara Diablo Creek

139

CA10165 Lewiston Trinity Trinity River CA00090 Long Valley Mono Owens River CA00887 Lopez San Luis Obispo Arroyo Grande Creek Los Banos Creek CA10167 Merced Los Banos Creek Detention Dam CA00127 Lower Crystal Springs San Mateo San Mateo Creek CA00635 Lower Kinney Lake Alpine Tr Silver Creek Lower San Fernando CA00076 Los Angeles San Fernando Creek (Lower Van Norman) CA00644 Lower Twin Lake Mono Robinson Creek CA00027 Madera Lake Madera Fresno River CA00739 Malibu Lake Club Los Angeles Malibu Creek CA10108 Martis Creek Nevada Martis Creek CA00212 Mathews Riverside Trib Cajalco Creek CA00312 Matilija Ventura Matilija Creek CA00459 McBrien Modoc Pit River CA10169 McGinty Modoc Mud Creek Mendota Diversion CA00886 Fresno San Joaquin River (Mendota Pool) CA10325 Miners Ravine Detention Modoc Trib Clover Swale Creek CA01122 Mission Viejo, Lake Orange Oso Creek CA00305 Mockingbird Canyon Riverside Mockingbird Canyon CA00243 Modesto Res Stanislaus Trib Tuolumne River CA10021 Mojave Dam San Bernardino W Fk Mojave River CA00110 Morena San Diego Cottonwood Creek CA00216 Morris Los Angeles San Gabriel River CA00155 Municipal Solano Trib Suisun Creek CA01013 Murry Santa Clara Mississippi Creek CA00812 Nacimiento San Luis Obispo Nacimiento River CA01029 Nash Shasta Trib Stillwater Creek CA10109 New Hogan Dam Calaveras Calaveras River CA10246 New Melones Calaveras Stanislaus River CA01082 New U San Leandro Alameda San Leandro Creek CA00156 Newell Santa Cruz San Lorenzo River CA10174 Nimbus Sacramento American River CA00321 Novato Creek Marin Novato Creek CA00847 Paicines San Benito Trib Tres Pinos Creek CA00475 Payne Modoc Trib South Fork Pit River CA00301 Peoples Weir Kings Kings River CA00208 Peters Marin Lagunitas Creek

140

CA00746 Peters Canyon Orange Peters Canyon CA00206 Phoenix Lake Marin Ross Creek CA00801 Pigeon Pass Riverside Pigeon Pass CA00128 Pilarcitos San Mateo Pilarcitos Creek CA10112 Pine Flat Fresno Kings River CA00098 Pleasant Valley Inyo Owens River CA00916 Poison Springs Modoc Rock Creek CA00743 Potrero Los Angeles Potrero Valley CA00909 Poway San Diego Warren Canyon CA00799 Prenda Riverside Prenda Creek CA10179 Prosser Creek Nevada Prosser Creek CA00194 Puddingstone Los Angeles Walnut Creek CA10180 Putah Diversion Yolo, Solano Putah Creek CA00771 Quail Valley Riverside Trib San Jancinto River CA00765 Railroad Canyon Riverside San Jacinto River CA01215 Ramona San Diego Green Val Road Creek CA00761 Rancho Cielito San Bernardino Trib Chino Creek CA00825 Rancho Seco Sacramento Trib Hadselville Creek CA00011 Rector Creek Napa Rector Creek CA00837 Redbank Fresno Redbank Creek CA00223 Robert A Skinner Riverside Tucalota Creek CA00485 Roberts Modoc Trib Pit River CA00262 Rodden Lake Stanislaus Lesnini Creek CA01351 Rubber Dam 1 Alameda Alameda Creek CA01380 Rubber Dam 2 Alameda Alameda Creek CA01251 Rubber Dam 3 Alameda Alameda Creek CA10202 Salinas San Luis Obispo Salinas River CA00620 Salt Springs Valley Calaveras Rock Creek CA00129 San Andreas San Mateo Trib San Mateo Creek CA00813 San Antonio Monterey San Antonio River CA00906 San Dieguito San Diego Trib Escondido Creek CA00200 San Gabriel Los Angeles San Gabriel River CA10323 San Justo San Benito Offstream San Lorenzo Creek (Don CA00841 Alameda San Lorenzo Creek Castro) CA00166 San Pablo Contra Costa San Pablo Creek CA00113 San Vicente San Diego San Vicente Creek CA00854 Sand Canyon Orange Sand Canyon CA10024 Santa Fe Los Angeles San Gabriel River

141

CA00298 Santiago Creek Orange Santiago Creek CA00563 Scout Lake Mendocino Trib Berry Creek CA00669 Searsville San Mateo Corte Madera Creek CA10025 Sepulveda Los Angeles Los Angeles River CA10324 Seven Oaks San Bernardino Santa Ana River CA00705 Sierra Vista Madera Chowchilla River CA01083 Soulajule Marin Arroyo Sausal CA00957 Spooner Lassen Trib Ash Creek CA10192 Stampede Sierra Little Truckee River CA10113 Success Tulare Tule River CA00873 Sulphur Creek Orange Sulphur Creek CA00800 Sycamore Riverside Sycamore Canyon CA01266 Sycamore Canyon Ventura Sycamore Can CA00729 Tejon Storage 2 Kern Trib Tejon Creek CA00888 Terminal San Luis Obispo Trib Arroyo Grande CA10114 Terminus (Lake Kaweah) Tulare Kaweah River CA00084 Tinemaha Inyo Owens River CA01115 Top Cat Tehama Trib Brannin Creek CA01123 Trampas Canyon Orange Trampas Canyon CA10196 Trinity Trinity Trinity River CA00956 Tule Lake (Moon Lake) Lassen Cedar Creek CA00905 Turner San Diego Moosa Canyon CA10308 Twin Lakes Mono Mammoth Creek CA10197 Twitchell San Luis Obispo Cuyama River CA01145 Upper Oso Orange Oso Creek CA00770 Vail Riverside Temecula Creek CA0029 Vasona Percolating Santa Clara Los Gatos Creek CA00750 Veeh Orange Trib San Diego Creek CA00829 Villa Park Orange Santiago Creek CA01314 Wallace Calaveras Trib Bear Creek CA10303 Warm Springs Sonoma Dry Creek CA00300 West Valley Modoc West Valley Creek CA00904 Westlake Reservoir Los Angeles Tree Springs Creek CA00029 Whale Rock San Luis Obispo Old Creek CA10027 Whittier Narrows Dam Los Angeles San Gabriel River CA00586 William, Lake Napa Trib Milliken Creek CA00850 Wood Ranch Ventura Trib Arroyo Simi CA00285 Woodbridge Div San Joaquin Mokelumne River

142

CA00796 Woodcrest Riverside Woodcrest Creek CA00276 Woodward Stanislaus Simmons Creek

143

ERRATUM

This December 12, 2014 release of the report, Assessing flows for fish below dams: a systematic approach to evaluate compliance of California’s dams with Fish and Game Code Section 5937, corrects or clarifies the following items in the original October 22, 2014 release:

 There are more than 6,200 documented barriers to fish passage in California and an additional 6,000 barriers with the potential to block fish passage.  Figure 34 identifies the main river above Pine Flat Dam as the Kings River.  Table 14 describes the attributes of Dwinnell Dam.