LOWER CHEHALIS RIVER AND SURGE PLAIN FISH USE ASSESSMENT

May, 2015 James Fletcher, Todd Sandell and Andrew McAninch

Prepared for: The Rose Foundation

Table of Contents 1.0. INTRODUCTION ...... 3

2.0. BACKGROUND AND PURPOSE ...... 3

2.1. SEA LEVEL RISE IN GRAYS HARBOR ESTUARY ...... 3 2.2. SPECIFIC OBJECTIVES ...... 5 2.3. SAMPLING GOALS ...... 5 3.0. STUDY AREA ...... 6

3.1. SALMON STOCKS ...... 6 3.2. CHEHALIS RIVER SURGE PLAIN AND LOWER RIVER ...... 7 4.0. FIELD SAMPLING METHODOLOGY ...... 9 4.1. FISH DATA ...... 10 4.2. DATA RECORDING/WATER QUALITY MEASURES ...... 10 4.3. AGE CLASS ASSIGNMENTS ...... 11 4.4. CATCH CALCULATIONS/ FISH DENSITIES ...... 11 5.0. RESULTS ...... 12

5.1. CATCH TOTALS ...... 12 5.2. HATCHERY RECOVERIES ...... 15 5.3. SALMON GROWTH/AGE CLASS ...... 15 5.3.1. Chinook Salmon ...... 16 5.3.2. Coho Salmon ...... 18 5.4. SALMON DISTRIBUTION AND TIMING (DENSITIES) ...... 19 5.4.1. Chinook salmon ...... 19 5.4.2. Coho salmon ...... 20 5.4.3. Chum salmon ...... 20 6.0 SUMMARY ...... 24 ACKNOWLEDGEMENTS...... 27 REFERENCES...... 27 APPENDIX 1. Chinook and Coho Salmon Fork Length Age Class Cutoffs (mm) ...... 30 APPENDIX 2. Sampling Sites ...... 30 APPENDIX 3. Stream Flow...... 31 APPENDIX 4. Summary of Factors Effecting Fish Abundance and Presence in Grays Harbor 2011 – 2013 ...... 32 APPENDIX 5. Water Temperature by Site ...... 33

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1.0. INTRODUCTION

The Chehalis River and Estuary are part of the range of habitats that salmon originating from the Chehalis River and its tributaries use during their life cycle. As such, juvenile salmon originating from the extensive network of rivers and streams in Water Resource Inventory Areas (WRIAs) 22 and 23 must all use some portion of the freshwater, estuarine and nearshore habitats in the Grays Harbor as they emigrate to the ocean.

Estuarine environments are extremely productive habitats and provide four main functions for juvenile salmon: growth and rearing, physiological transition from freshwater to saltwater, migratory pathways to the ocean, and predator avoidance (Simenstad et al. 1982). Estuarine habitats vary in their ability to support these functions as a result of natural and anthropogenic variability in the qualities of the habitat. Understanding how well the lower Chehalis River and the transition zones to estuarine habitats support these functions is a critical component in the development of a salmon restoration strategy for the entire basin.

2.0. BACKGROUND AND PURPOSE

In 2011 Wild Fish Conservancy began research to understand how the estuarine habitats in Grays Harbor are utilized by emigrating juvenile salmon (Grays Harbor Juvenile Fish Use Assessment, Sandell et al. 2014). Understanding the relationship between salmon and their habitats is the foundation for developing a restoration strategy to ensure the viability and persistence of salmon populations. Our objectives were to document how fish utilize the variety of estuarine habitats associated with Grays Harbor as they emigrate to the sea, or, in some cases, rear in the estuary for up to a year. This work also led us to seek support from the Rose Foundation to investigate the lower mainstem Chehalis River, to better understand the timing of emigration, the habitats most utilized by juvenile salmon, and the environmental variables found in the lower river.

2.1. SEA LEVEL RISE IN GRAYS HARBOR ESTUARY

In 2012, concerned with the potential for sea level rise to severely alter habitat availability in the Grays Harbor estuary as well as to undermine many of the habitat restoration projects planned for the area, Wild Fish Conservancy conducted a modeling

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of climate change in the Chehalis Basin (Sandell & McAninch, 2013). Using the Sea Level Affecting Marshes Model (SLAMM), we analyzed the estuary with regard to sea level rise (SLR) under different climate change scenarios proposed by the Intergovernmental Panel on Climate Change (IPCC). The model predicted rapid changes in the upper estuary, specifically the freshwater tidal Surge Plain (Figure 1), “[which will] transition from forested tidal swamp to irregularly flooded marsh by 2025 even in the most conservative scenario; the net loss of forested area is predicted to be severe (~97% for the estuary as a whole).” The vast majority of forested area in the estuary is found in the Surge Plain, where the lower Chehalis River becomes tidally influenced. The predicted changes in the present day Surge Plain, due in part to the encroachment of a salt water “wedge” that may kill the large trees and undermine the stability of the many off- channel sloughs in the area, could dramatically alter the habitat and migration corridor utilized by juvenile salmon. For this reason, we are now focused on understanding where the future Surge Plain is likely to occur and how juvenile salmon are currently utilizing this area, so that conservation managers can make effective planning decisions that addresses climate change well into the future.

Figure 1. Mean High Water levels for the Surge Plain under 5 sea-level rise scenarios (0.59, 0.75, 1.0, 1.25, and 2.0 meter rise);calculated with a DEM processed to correct for high water levels during some of the dates LiDAR was acquired.

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2.2. SPECIFIC OBJECTIVES

The Lower Chehalis River and Surge Plain Fish Use Assessment was developed as a pilot study, conducted by the Wild Fish Conservancy with funding provided by the Rose Foundation. The primary goals were to anticipate the location and extent of the future Surge Plain and to identify the key habitat areas utilized by juvenile salmon and other fishes. The project had four specific objectives at the outset:

1. Estimate the future head of tidal intrusion and map the habitats of the lower river using 2013 LiDAR data. (Accomplished in July, 2014) 2. Determine the abundance, distribution, emigration timing and habitat preferences of juvenile salmonids in the Surge Plain and lower Chehalis River. Meeting this objective also establishes the presence of these fish at locations in the lower river, a prerequisite for land acquisition for conservation or conservation easements. 3. Understand which physical variables (flow rate, dissolved oxygen, temperature, salinity) best predict the distribution of Chinook, coho, and chum salmon, and which habitat types are of the highest priority. 4. Integrate this knowledge into the Grays Harbor Estuary Salmonid Conservation Plan, which identifies specific restoration and conservation opportunities in the estuary, Surge Plain and lower Chehalis River.

2.3. SAMPLING GOALS

Our plan at the outset was to sample 15-18 sites via beach seining once a month from March through August, 2014. An additional sampling trip in October or November, following the first major rain event of the fall, would target juvenile salmonids returning upstream from the estuary to document the presence of alternative coho salmon life histories that utilize the estuary in summer and overwinter in protected habitats in the Surge Plain. Due to funding constraints not all of these goals could be met; instead, sampling efforts were restricted to 3 sessions, April 18-23, June 11-13, and July 23-25, during low tide series. In April, during our initial sampling effort, the Chehalis River discharge was high, between 3500 and 5000 cfs (Appendix 3); this limited the locations we could sample and our ability to determine if the same sites could be sampled at lower

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flows. In total, we conducted 106 beach seine sets at 26 sites, 16 of which were sampled every sampling session (Figure 3, Appendix 2).

Our approch to objective 3 (identify which physical variables best predict the distribution of Chinook, coho, and chum salmon, and which habitat types are of the highest priority) was to construct a separate series of of generalized linear regression (GLM) models relating species abundance and occurrence to spatial, habitat, environmental and temporal variables. We have previously used this data exploration approach to achieve a similar objective in the main estuary in 2011 – 2013. Some of these results apply to habitat utilization in the Surge Plain and to a lesser degree, the lower river (Appendix 4). They include: species-specific relationships to habitat and environmental variables, migration timing, and distribution and abundance at three sample sites located in the Surge Plain and one site near the mouth of the Wynoochee River.

3.0. STUDY AREA

Grays Harbor (the Chehalis River estuary) is the second largest estuary in the state of Washington after the Columbia River estuary. The Grays Harbor estuary is a bar-built estuary that was formed by the combined processes of sedimentation and erosion caused by both the Chehalis River and the Pacific Ocean (Chehalis Basin Habitat Work Group, 2010). The estuary covers 23,504 hectares at mean high high-water (MHHW) from the mouth at Westport to Montesano, and encompasses the tidally influences lower reaches of the Chehalis, Humptulips, Hoquiam, Wishkah, Johns and Elk Rivers as well as several smaller tributaries. The total drainage area, including all of the above tributaries, is 660,450 hectares, with 79% of the fresh water input from the Chehalis River (Simenstad & Eggers 1981). The system flows are rainfall driven, with peak flows from December- January in an average year, and minimal input from snowmelt in the southern Olympic Mountains (snowmelt drainage occurs primarily through the Satsop River basin).

3.1. SALMON STOCKS

Within the Chehalis basin there are numerous distinct stocks of native salmonids that are important to the overall biological diversity in Washington State. These include one stock of spring Chinook salmon (Oncorhynchus tshawytscha), one stock of summer Chinook,

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seven stocks of fall Chinook, seven stocks of coho salmon (O. kisutch,) two stocks of fall chum salmon (O. keta), two stocks of summer steelhead trout (O. mykiss), and eight stocks of winter steelhead (WDFW and WWTIT 1994). In addition, cutthroat trout (O. clarki) have been observed throughout the drainage, and bull trout (Salvelinus confluentus) have been documented as present, but specific distribution data do not exist. All of these stocks have been in decline, as have most salmonid stocks in the Pacific Northwest, though none are presently listed as threatened or endangered under the Endangered Species Act.

3.2. CHEHALIS RIVER SURGE PLAIN AND LOWER RIVER

Although much of the basin has been degraded by a combination of logging, channelization, gravel mining, water diversion, road building, diking, dredging, aquaculture, small-scale coal mining, mill effluent, sewage release and pesticide use for aquaculture and cranberry farming (Hiss et al. 1982; Wood & Stark 2002; Smith & Wenger 2001) , the area of the lower mainstem Chehalis River, the tidal Surge Plain (river km 1-17, just east of Aberdeen to the confluence of the Wynoochee River), contains high-quality rearing habitat for juvenile salmon, particularly coho, and has been well studied (Moser et al. 1991; Simenstad et al. 1992; Team 1997; Hood 2002; Henning et al. 2006; Henning et al. 2007). This area contains numerous sloughs and tidal channels, a relatively undeveloped floodplain with seasonal inundation, and a riparian forest dominated by older stands of conifers and hardwoods that largely escaped logging due to its challenging terrain (Ralph et al. 1994). Because of its significance as off- channel rearing habitat and refugia from high winter flows for juvenile salmon, a large part of the Surge Plain has been protected. However, in the coming decades the area will be affected by sea level rise (SLR) due to climate change.

Agriculture occurs in the valleys upstream of Montesano, with timber production on the moderately steep slopes (Phinney and Bucknell 1975). Poor floodplain conditions exist in the stretches between Montesano and the Satsop River (one of the largest sub-basins in the drainage) and between the Satsop confluence and Elma due to bank protection (levees) and channelization. The upper extent of most of the chum spawning habitat is in this region, near the mouth of Cloquallum Creek. The causes of floodplain impacts, such

Lower Chehalis River Juvenile Fish Use Assessment, 2015 Wild Fish Conservancy Page 7 as channel incision or loss of side-channel habitat, are poorly documented, but likely causes include bank hardening, filling and draining of wetlands, increased sediment transport (leading to channel incision), and the loss of large wood.

Upstream of Elma, the mainstem has both spawning and rearing habitat for salmon, although the mainstem spawning habitat is used mostly by chinook (Smith & Wenger 2001). Coho salmon and steelhead trout use the mainstem for transportation to spawning areas, and also rear in the sloughs and off-channel habitat.

Figure 2. Map of the Lower Chehalis River study reach, Washington State, U.S.A.

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4.0. FIELD SAMPLING METHODOLOGY

We sampled the lower Chehalis River habitats using a modified version of methods used by Wild Fish Conservancy in other habitat use assessments. A small, fine-mesh beach seine was used to sample river shorelines and freshwater tidal sloughs. The areas sampled were typically less than 5 feet deep (1.5 m). The beach seine uses an 80-foot (24.4 m) by 6-foot (1.8 m) by 1/8-inch (0.3 cm) mesh knotless nylon net. The net is set by fixing one end on the beach, deploying the rest of the net off the bow of the skiff at an angle slightly upstream of perpendicular to the beach (to adjust for downstream drift of the skiff) and towed back to shore in a quarter circle. A tow line (bridle) is attached to the tow end of the net to facilitate deployment. Both ends of the net are then retrieved, yielding a catch. We typically conducted two adjacent sets per site to provide a measure of catch variability. Average set area was 467 square meters (0.047 ha).

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Figure 3. Location of the sample sites and the frequency which they were sampled.

4.1. FISH DATA

All fish captured were enumerated, identified to species, and visually scanned for the presence/absence of an adipose fin to determine their origin (hatchery vs. wild). The first 20 individuals of each species/age class/mark status captured at a site were measured for fork length (mm). All Chinook and coho salmon were scanned for coded wire tags (CWT), and those found with tags were sacrificed for tag extraction in order to determine release location, release date, and river basin of origin.

4.2. DATA RECORDING/WATER QUALITY MEASURES

For each sampling set, we recorded data on time of day, percent of net haul utilized in the set (with few exceptions, 100% of the net was utilized; in some cases a smaller percentage was “fished”) and duration of the net set (used in reviewing the data to determine if the net was fished for an unusually long time due to snags, resulting in that particular set being excluded from quantitative analysis). Water quality parameters were measured at each site: temperature and salinity were measured using a water meter (Yellow Springs Instrument Co., Yellow Springs, Ohio); dissolved oxygen was measured using a multi-parameter field meter (Geotech Environmental Equipment, Inc., Boulder,

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Colorado); and water flow measurements were carried out using a 3D acoustic Doppler velocimeter (ADV) (Sontek Instruments, San Diego, California).

4.3. AGE CLASS ASSIGNMENTS

To differentiate between subyearling and yearling Chinook and coho salmon, we examined the fork length (mm) distributions of catch by species and month. The length classes were quite distinct (Appendix 1), with few fish falling in borderline length ranges. Based on our sampling protocol and time limitations in the field to process large catches, only the first 20 of each species/mark status (hatchery or wild, i.e. marked or unmarked) were measured for fork length.

4.4. CATCH CALCULATIONS/ FISH DENSITIES

All data were originally recorded on a standardized data form in the field; subsequently data from the field forms were entered into a Microsoft Access database for analysis. Catch data were double checked and all data reviewed for QA/QC. These data are summarized as raw catch numbers and catch densities, calculated in hectares (below), and organized by species, sample site and date.

At each site at least two consecutive seine hauls were conducted per sampling event, so density was calculated as the summed catch of the net sets (total catch of species y), divided by the sum total area of the consecutive net sets, to get the catch per meter squared.

To calculate the density of a given species (or age class of a species) in hectares (1 hectare = 10,000 m2), the formula is:

= × 10,000 ( m2) �푡�푡푡 푐𝑐푐ℎ �표 �푠𝑠𝑠� 푌 퐷퐷퐷퐷퐷퐷퐷 This is equivalent to the concept of� catch푡�푡푡 𝑛�per �unit푎𝑎 effort (CPUE), with the number of sets made and the area of the net used taken into account, to normalize the catch data by area sampled. On rare occasions where the net was deployed to a greater or lesser extent than normal, we corrected the standard net area with an estimated fraction of the area sampled.

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Note: Sampling effort varied between field visits because of changes in river discharge and river height, and the gradual refinement of our sampling strategy and site list.

5.0. RESULTS

5.1. CATCH TOTALS Data presented in this section refer to actual catch numbers; note that in the following sections that deal with salmon densities by site, catch densities are presented by catch per hectare, and are thus adjusted by the multiplication factor required since our nets sample only a fraction of a hectare (ha). See Density Calculations (above) for more information.

During the three sampling sessions (April 18-23; June 11-13; July 23-25), we caught a total of 16,141 fish; consisting of 21 different species (six others were unidentified due to their small size and/or larval state, e.g. “post larval minnow”). Three species of salmon

Lower Chehalis River Juvenile Fish Use Assessment, 2015 Wild Fish Conservancy Page 12 were captured (chum, coho, and Chinook salmon), as well as several rainbow trout/steelhead and cutthroat (Figure 4). The most abundant species by far were three- spine stickleback, accounting for 56% of the catch. The next most abundant species were Chinook salmon and northern pikeminnow, accounting for about 13% and 8% of the total catch respectively. Together, these three species made up roughly 77% of the catch.

Figure 4. Lower Chehalis River catch totals for 2014, by species

As Figures 4 & 5 show, salmon made up a relatively small portion of the fish captured; Chinook being the most abundant primarily during the late April sampling session. However, the composition of the fish assemblage changed dramatically between April and July; salmon accounted for about 63% of all fish in April, but just 3% in June and 1% in July. Chum salmon were present only in April and would likely account for a much larger portion of the fish assemblage if sampling had begun earlier in the year; peak outmigration in the estuary occurred in March and April, with chum largely absent from the Surge Plain by May (Sandell et al., 2014). Coho salmon made up only a minor

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portion of the catch in all months (catch totals: YOY, n= 58; yearling, n=29), despite being the most numerous salmonid in terms of adult returns to the Chehalis River. The low abundance indicates that YOY coho do not utilize the mainstem river sites or freshwater tidal sloughs in the lower Chehalis to the same degree as Chinook salmon, but use side-channel habitats and to a lesser extent seasonal wetlands instead (Henning 2004).

For yearling coho, this low abundance may be an artifact of sampling by beach seine, which does not effectively sample the deeper channels yearling salmon occupy. Yearling coho, as anticipated, were present only in the April sampling session with the exception of a single fish in June. Data from the Grays Harbor Estuary Juvenile Fish Assessment show that yearling coho are present in the estuary primarily in April and May. By June and July, the abundance of several other species had increased (primarily stickleback, but also pikeminnow, peamouth, red-sided shiner and juvenile starry flounder), coinciding with warmer water temperatures and lower river flows (Appendices 3 & 5).

Figure 5. Lower Chehalis River species composition (%) and catch total (data labels) by sampling session, 2014

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5.2. HATCHERY RECOVERIES

An estimated 99.5% of Chinook salmon, 80% of Coho salmon, and 87% of steelhead trout released from hatcheries in the Chehalis basin were adipose fin clipped in 2014 (data: Pacific States Marine Fisheries Commission, Regional Mark Processing Center). A small number of juvenile hatchery fish were captured during this project: nine juvenile steelhead trout, two yearling coho and one Chinook salmon. A single coded wire tag (CWT) was recovered from an adipose clipped coho salmon on April 28, 2014. The CWT was extracted and matched to the Pacific States Marine Fisheries Commission Regional Mark Information System (RMIS) database; analysis of the tag showed it originating from WDFW’s Skookumchuck Hatchery, entering the Chehalis River near Centralia.

5.3. SALMON GROWTH/AGE CLASS

In general, residence time in the estuary decreases as the size of the fish entering the estuary increases. Young-of-the-year (YOY; also referred to as age 0+, or subyearlings) tend to spend more time in estuarine waters and are thus more dependent on estuarine habitats than larger juveniles (“yearlings”; age 1+), which typically reside in streams for their first year of life prior to smolting, when they rapidly emigrate to sea. These classifications apply mainly to Chinook and coho salmon, which have the most diverse patterns of estuarine usage (Zaugg et al. 1985; Moser et al. 1991; Bottom et al. 2005; Hering et al. 2010) chum salmon migrate directly to the sea shortly after hatching in early Spring and are thus all YOY (few hatchery chum salmon in the Chehalis Basin are marked, so all chum were considered “unmarked”, although in recent years ~5% were of hatchery origin; data from WDFW). Steelhead trout, which typically rear in freshwater for 1-3 years (Quinn 2005), were all considered yearlings or older.

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Figure 6. Juvenile salmon size trends from all 24 sites combined in the lower Chehalis River in 2014.

5.3.1. Chinook Salmon

Chinook salmon populations are generally classified as one of two life history types: yearling migrants (stream-type) – those that spend one year or longer in freshwater and tend to pass quickly through estuaries; or YOY migrants (ocean-type) – those that migrate to sea early in their first year of life after spending only a short period (or no time) rearing in freshwater. Both this study and the Grays Harbor Estuary Juvenile Fish Use Assessment indicate that YOY migrants (ocean-type life history) predominate the juvenile outmigration; all of the Chinook salmon captured in this study and more than 99.9% of Chinook captured in the estuary assessment were YOY. It should be noted that the sampling method likely biased our catch – beach seining from shore does not adequately sample deeper water depths where larger yearling Chinook salmon are likely to reside. Juvenile salmon are generally distributed based upon water depth, with the depth of the water occupied by the fish increasing as the size of the fish increases (McCabe et al. 1986).

Salmonids are “phenotypically plastic generalists”, meaning they have highly variable life-history strategies. Within stream or ocean-type life histories individuals exhibit a

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variety of alternative spatial and temporal life history strategies in their use of available habitat. Although any Chinook salmon population can potentially produce all life history strategies, some strategies will be more abundant than others within a population. By examining juvenile Chinook size at estuarine entry and arrival time in the estuary, we can define the YOY, ocean-type Chinook population as early and late migrants based on the population’s length trend (Figure 7). Size upon arrival in the estuary can be used to classify life history strategy because there is a relationship between fish size, habitat use, and residence time (Simenstad et al. 1982, Levings et al. 1986, Tschaplinski 1987, Beamer 2005). Generally, early migrants are smaller, while late migrants are larger. The later migrants are larger in size because of their longer rearing period in the freshwater environment. Based upon these observations, the majority of juvenile Chinook captured in lower Chehalis River in 2014 (April sampling effort) were early migrants (Figure 6); spending only a short period (or no time) rearing in freshwater. By contrast, the total catch of late-migrant/river rearing Chinook in June was just 9% of the April Chinook catch (Figure 4). The proportion of the population that exhibit early migration may be a result of overall population size and a limitation in freshwater habitat capacity (Beamer 2005); as freshwater habitat fills up, the excess fish respond by moving downstream.

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Figure 7. Length trend of subyearling Chinook salmon moving through a sample site in lower Chehalis River in 2012. Fish captured before day 128 (early May) were similar in size, reflecting a population that migrated relatively quickly following emergence. After day 128 the length of juvenile Chinook salmon steadily increased, reflecting riverine growth.

5.3.2. Coho Salmon

Despite the fact that coho are the most numerous salmon species in terms of adult returns, only a few juvenile coho were captured during the course of the study, indicating that YOY coho do not utilize the lower Chehalis River mainstem to the same degree as Chinook salmon. Furthermore, the average length of YOY coho changed very little between sampling efforts in April and June (Figure 6): the average length of YOY coho in April went from 39.2 mm (SD = 2.8) to 44.1 mm (SD = 4.9) in June, which points to little or no rearing in the mainstem river, but instead the presence of migrating fry. In comparison, the average length of juvenile Chinook, increased from 43.5 mm (SD = 4.6) to 61.9 mm (SD = 12.0) over the same period. There is good evidence that these migrating coho fry exhibit an estuarine-rearing life history strategy (Craig et al. 2014) which enables them to take advantage of more productive tidal wetland habitats downstream. In 2011, fyke net sampling of estuarine sloughs in Grays Harbor

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demonstrated a high abundance of estuarine-rearing YOY coho salmon in eulittoral marsh habitats; specifically intertidal sloughs with some freshwater input and horizontal salinity gradients (Grays Harbor Estuary Salmonid Conservation Plan, 2015). This highlights the importance of tidal wetlands to local coho salmon populations, their life- history diversity and their adaptive capacity to be more ecologically resilient to environmental uncertainty (Healey 2009).

5.4. SALMON DISTRIBUTION AND TIMING (DENSITIES)

To visualize the timing of our salmonid catches in the lower Chehalis River and Surge Plain, we generated plots showing catch densities (not actual catch numbers) for juvenile Chinook, coho, and chum salmon (Figures 8-11). They are presented in order by sampling session to show discrete “snapshots” of distribution over time. Note that the number of plots differ by species because zero catches were not plotted (e.g. chum were absent after April, and yearling coho were absent in July).

5.4.1. Chinook salmon

All of the Chinook salmon captured in this study and more than 99.9% of Chinook captured in the Grays Harbor Estuary Juvenile Fish Use Assessment were YOY (ocean type) life histories (Note: it is likely that the beach seining method employed does not sample deeper water where larger yearling salmon are more likely to reside). In April, high densities of early fry migrant Chinook were observed throughout the study reach, with the highest densities (>800 fish/ha) most frequently occurring in the lower Chehalis River, and slightly lower overall densities (ranging from 100-200 to 800+ fish/ha) occurring in the Surge Plain (Figure 8). By June, the early migrant Chinook had exited the lower Chehalis River and Surge Plain into the main estuary. The remaining late migrant Chinook, which display some degree of riverine rearing (as evidenced by growth), were patchily distributed throughout the study area (0 to 400-800 fish/ha), and absent in some locations. By the end of July, Chinook were absent at over one-third of the sites and present in low densities at the remaining sites, some of which were upriver (near the confluence with Porter Creek).

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5.4.2. Coho salmon

The total number of coho salmon was about 3% that of Chinook salmon and coho densities were also many times smaller. YOY coho, essentially all of which are unmarked in the Chehalis Basin, were encountered occasionally and usually in low densities with one exception, the sampling site “Cow Run” near the mouth of Delzene Creek on June 16 (>800 fish/ha) (Figure 9). This high density coincided with a notably cooler water temperature at this site (14.1°C) compared to the average water temperature of 8 other locations that day (17.1°C ± 0.25). Cooler water temperature may indicate the presence of hyporheic groundwater upwelling which might be actively sought after by juvenile coho during summer months (cold groundwater may be a limiting resource in summer, and resource managers should consider prioritizing such areas for protection and restoration). By late July, coho were absent from all sites except for 3 individuals at the mouth of the Satsop River, which is also a source of cooler than average water (Appendix 5).

Almost all yearling coho were captured during the April sampling session; this concurs with data from the Grays Harbor Estuary Juvenile Fish Assessment (yearling coho were present in the estuary primarily in April and May). In the lower Chehalis and Surge Plain, yearling coho were captured in low densities at just six sites (Figure 10).

5.4.3. Chum salmon

Based on their life history, chum salmon fry typically migrate quickly from their natal stream and enter the estuary in winter; data from the 2011-’13 estuary study show that chum were largely absent from the Surge Plain by May. Chum salmon were only captured in April, as expected, and in varying densities at three sites in the Surge Plain, but none in the lower river (Figure 11).

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Figure 8. Density and distribution of juvenile Chinook salmon in the lower Chehalis River, 2014.

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Figure 9. Density and distribution of YOY coho salmon in the lower Chehalis River, 2014.

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Figure 10. Density and distribution of yearling coho salmon in the lower Chehalis River, 2014.

Figure 11. Density and distribution of juvenile chum salmon in the lower Chehalis River, 2014.

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6.0 SUMMARY

The primary goals of this study were to identify the key habitat areas utilized by juvenile salmon and other fishes in the lower mainstem Chehalis River and Surge Plain. In addition, we anticipated the location and extent of the future Surge Plain, as well as investigating habitat utilization and environmental variables found in the lower river. Due to funding constraints (the U.S. Fish and Wildlife Service elected not to fund the 2014 work, although we are grateful for their support of the estuary study) some of these goals could not be met; instead, sampling efforts were restricted to 3 sessions, April 18-23, June 11-13, and July 23-25, during low tide series.

During the three sampling sessions we caught over 16,000 fish, consisting of 21 different species. This included three species of salmon (chum, coho, and Chinook salmon), as well as several rainbow trout/steelhead and cutthroat. Salmon made up a relatively small portion of the total catch (15%); however, the composition of the fish assemblage changed dramatically between April and July. In April, salmon accounted for about 63% of all fish (primarily Chinook salmon), by June and July, salmon comprised less than 3% of the catch. The increased abundance of stickleback (56% of total catch), pikeminnow (8%), peamouth, red-sided shiner and juvenile starry flounder coincided with warmer water temperatures and lower river flows. Together, stickleback, Chinook salmon and northern pikeminnow made up roughly 77% of the total catch. Three species of non-indigenous fish - largemouth bass, smallmouth bass and yellow perch - were also recorded in low numbers (combined total = 10).

The tidal Surge Plain, which begins just east of Aberdeen and extends to the confluence of the Wynoochee River, contains high-quality rearing habitat for juvenile salmon, particularly coho, and has been well studied. This area contains numerous sloughs and tidal channels, a relatively undeveloped floodplain with seasonal inundation, and a riparian forest dominated by older stands of conifers and hardwoods that largely escaped logging due to its challenging terrain. Because of its significance as off-channel rearing habitat and refugia from high winter flows for juvenile salmon, 3,018 acres have been designated a Natural Area Preserve (NAP), by Washington State Department of Natural Resources. However, in the coming decades the area is predicted to be affected by sea level rise (SLR) due to climate change.

Poor floodplain conditions exist in the stretches upstream of Montesano and between the Satsop confluence and Elma due to bank protection and channelization. The upper extent of most of the

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chum spawning habitat is in this region, near the mouth of Cloquallum Creek. The causes of floodplain impacts, such as channel incision or loss of side-channel habitat, are poorly documented, but likely causes include bank hardening, filling and draining of wetlands, increased sediment transport (leading to channel incision), and the loss of large wood. Upstream of Elma, the mainstem has both spawning and rearing habitat for salmon, although the mainstem spawning habitat is used mostly by Chinook (Smith & Wenger 2001). Coho salmon and steelhead trout use the mainstem for transportation to spawning areas, and also rear in the sloughs and off-channel habitat.

Our research has specific implications for salmon recovery planning and restoration actions in the lower Chehalis River and Surge Plain. Juvenile salmon utilize the lower Chehalis River and Surge Plain extensively, with salmon caught at all the sample sites. Survival during this early period of their life-cycle is critical for the overall success of their respective populations. Juvenile salmon using these areas experience different levels of survival due to differences in their migration timing, location, and duration of habitat use.

• Chinook Salmon

Chinook salmon were the most abundant salmonid captured (n= 2,148) and were present during all three sampling sessions. In April, high densities of early fry migrant Chinook (spending only a short period, or no time, rearing in freshwater) were observed throughout the study reach, with the highest densities (>800 fish/ha) most frequently occurring in the lower Chehalis River, and slightly lower overall densities occurring in the Surge Plain. By June, the early migrant Chinook had exited the lower Chehalis River and Surge Plain into the main estuary, leaving the remaining late-migrant/river rearing Chinook which accounted for just 10% of the total Chinook catch. By the end of July, Chinook were absent at over one-third of the sites and present in low densities at the remaining sites. This illustrates the importance of both river and estuarine habitat to local Chinook salmon populations and their life-history diversity. Fry migrants and estuarine rearing fish, which are the dominant strategies at present, use the lower Chehalis River and Surge plain primarily as a migration corridor to gain access to estuarine and shoreline habitats early in the season. These habitats are at greatest risk of change by human land uses and should be considered a priority for protection and restoration actions. By contrast, late parr migrants rear for a couple of months in the lower Chehalis to achieve a similar size as their estuarine/delta

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rearing cohorts over the same time period. Habitat changes in the present day Surge Plain, due in part to sea level rise and the encroachment of the salt water “wedge”, will likely impact parr migrants more than early migrant life histories.

• Coho Salmon

Despite being the most numerous salmonid in terms of adult returns to the Chehalis River, coho salmon made up only a minor portion of the catch in all months (catch totals: YOY, n= 58; yearling, n=29). YOY coho were encountered occasionally and usually in low densities with one exception, a sampling site near the mouth of Delzene Creek in June where we recorded densities greater than 800 fish per hectare. The water temperature at this location was notably lower (14.1°C) than the water temperature of the 8 nearest sample sites (17.1°C ± 0.25). Cooler water temperature may indicate the presence of hyporheic groundwater upwelling which might be actively sought after by juvenile coho during summer months. Cold groundwater may be a limiting resource in summer, and resource managers should consider prioritizing such areas for protection and restoration.

The average length of YOY coho changed very little between sampling efforts in April and June, which suggests these fish may be early migrants, seeking out more productive tidal wetland habitats downstream. YOY coho did not utilize the mainstem river sites or freshwater tidal sloughs in the lower Chehalis to the same degree as Chinook salmon, but depend heavily on side-channel and off-channel rearing habitat and to a lesser extent seasonal wetlands (Henning 2004). Poor river-floodplain connectivity (mostly due to levees), particularly between the Satsop confluence and Elma, limit juvenile coho rearing habitat and should be considered high priority areas for restoration.

Yearling coho, as anticipated based on data from the estuary study, were present only in the April sampling session with the exception of a single fish in June. The low capture rate may be an artifact of sampling by beach seine, which does not effectively sample the deeper channels yearling salmon occupy.

• Chum Salmon

Chum salmon were captured only in April and only in the Surge Plain, as expected given a life history where chum salmon fry migrate quickly from their natal streams to the estuary during the

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winter months. Data from the estuary study (2011-’13) show that peak densities of chum salmon in the main estuary occurred in March/April and chum were largely absent from the surge plain by May. More data targeting the winter months would be required to understand the migration timing, location, and duration of habitat use for chum salmon in our study area.

ACKNOWLEDGEMENTS

A number of people were involved in the sampling effort for this project and we are indebted to them for their assistance in the field: Aaron Jorgenson, Adrian Tuohy, and Frank Staller (Wild Fish Conservancy), and Chris Rice, among others.

This project was funded by the Rose Foundation and is available online as a pdf at the Wild Fish Conservancy’s website: http://wildfishconservancy.org/projects/lower-chehalis-river-and-surge- plain-fish-use-assessment

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REFERENCES Beamer, E., Hayman, B., and Smith , D., 2005. Linking Freshwater Rearing Habitat to Skagit Chinook Salmon Recovery. Appendix C of the Skagit Chinook Recovery Plan. Skagit River System Cooperative, La Conner, WA.

Bottom, D.L. et al., 2005. Salmon at River’s End: The Role of the Estuary in the Decline and Recovery of Columbia River Salmon,

Craig B,E., Simenstad C,A. Bottom D, L. 2014. Rearing in natural and recovering tidal wetlands enhances growth and life-history diversity of Columbia Estuary tributary coho salmon Oncorhynchus kisutch population. Journal of Fish Biology (2014) 85, 31–51

Henning, J.A., Gresswell, R.E. & Fleming, I. a., 2007. Use of seasonal freshwater wetlands by fishes in a temperate river floodplain. Journal of Fish Biology, 71(2), pp.476–492.

Henning, J.A., Gresswell, R.E. & Fleming, I.A., 2006. Juvenile Salmonid Use of Freshwater Emergent Wetlands in the Floodplain and Its Implications for Conservation Management. North American Journal of Fisheries Management, 26(2), pp.367–376.

Healey, M. 2009. Resilient salmon, resilient fisheries for British Columbia, Canada. Ecology and Society 14(1): 2

Henning, Julie 2004. An Evaluation of Fish and Amphibian Use of Restored and Natural Floodplain Wetlands. Final Report EPA Grant CD-97024901-1. Washington Department of Fish and Wildlife, Olympia, Washington, USA. 81 p.

Hering, D.K. et al., 2010. Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel. Canadian Journal of Fisheries and Aquatic Sciences, 67(3), pp.524–533.

Hood, G.W. 2002. Application of Landscape Allometry to Restoration of Tidal ChannelsRestoration Ecology Vol. 10 No. 2, pp. 213–222

McCabe Jr., G.T., R.L. Emmett, W.D. Muir, and T.H. Blahm. 1986. Utilization of the Columbia River estuary by subyearling Chinook salmon. Northwest Science 60:113–124.

Moser, M.L., Olson, A.F. & Quinn, T.P., 1991. Riverine and estuarine migratory behavior of coho salmon (Oncorhynchus kisutch) smolts. Canadian Journal of Fisheries and Aquatic Sciences, 48(9), pp.1670– 1678.

Phinney, L.A. and P. Bucknell. 1975. A catalog of Washington streams and salmon utilization, Volume 2: Coastal Region. Washington Dept. Fisheries, Olympia, Washington.

Quinn, T.P., 2005. The behavior and ecology of Pacific salmon and trout, Bethesda, Maryland: American Fisheries Society and the University of Washington Press.

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Ralph, S.C., Peterson, N.P. & Mendoza, C.C., 1994. An inventory of off-channel habitat of the lower Chehalis River with applications of remote sensing.

Sandell, T., Fletcher, J., McAninch, A. & Wait, M., 2014. Grays Harbor Juvenile Fish Use Assessment: 2013 Annual Report.

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Simenstad, C.A., Fresh, K.L. & Salo, E.O., 1982. The role of Puget Sound and Washington coastal estuaries in the life history of Pacific salmon: An unappreciated function. In V. S. Kennedy, ed. Estuarine Comparisons. New York: Academic Press, pp. 343–364.

Smith, C.J. & Wenger, M. 2001 Salmon and Steelhead Habitat Limiting Factors - Chehalis Basin and Nearby Drainages. Washington State Conservation Commission Final Report

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Tschaplinski, P.J., 1987. The use of esturies as rearing habitats by juvenile coho salmon. In T. W. Chamberlin, ed. Applying 15 years of Carnation Creek Results. Nanaimo, B.C.: Pacific Biological Station, pp. 123–141.

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APPENDIX 1. Chinook and Coho Salmon Fork Length Age Class Cutoffs (mm)

Month Coho YOY ≤ Coho yearling ≥ Chinook YOY ≤ Chinook yearling ≥ February 70 100 March 70 100 April 80 100 May 90 110 June 130 130 July 130 140 August 130 150 September 130 165 October 130 175

APPENDIX 2. Sampling Sites

Site Name Latitude Longitude April June July Blue Slough 46.94622 -123.72 X X X Chinook eddy 46.95853 -123.696 X X X Preacher Slough 46.95049 -123.694 X X X Peels Slough 46.95727 -123.666 X X X Chehalis near restoration site 46.94757 -123.655 X X X Wynoochee beach (upstream) 46.97313 -123.616 X Wynoochee beach (downstream) 46.96786 -123.609 X Wynoochee delta 46.96257 -123.607 X X Highway 12 bridge 46.96316 -123.601 X X X Montesano bar 46.9666 -123.595 X X X Stewart Creek bar 46.9684 -123.561 X X Moon Slough pond 46.96737 -123.542 X Satsup bar 46.9754 -123.486 X Satsup confluence 46.97715 -123.484 X X X Lower Satsup 46.98215 -123.483 X X X Stewart Creek island 46.97888 -123.463 X X X Cottonwood bend 46.98153 -123.389 X X X Cow run 46.97187 -123.38 X Prickly eddy 46.95939 -123.362 X X Tarp beach 46.96554 -123.36 X X X Smith farm 46.95345 -123.353 X X X Bar above ramp 46.92279 -123.311 X X X Eagle bar 46.91276 -123.305 X X X Yellow flag 46.89789 -123.295 X Rock Creek 46.88086 -123.294 X X Cedar Creek bar 46.88553 -123.288 X X X

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APPENDIX 3. Stream Flow Chehalis River discharge at Porter (USGS 12031000), April – July, 2014 . http://waterdata.usgs.gov

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APPENDIX 4. Summary of Factors Effecting Fish Abundance and Presence in Grays Harbor 2011 – 2013

Unmarked Chinook Hatchery Chinook Unmarked Chum Water o Abundance negatively correlated with temp Temperature Salinity Habitat o Abundance negatively correlated with: o Abundance positively correlated with: . intertidal pebble, gravel and sand habitats . intertidal mixed fines . intertidal mixed fines/seasonal aquatic vegetation . intertidal pebble/gravel/sand Tide Height o Abundance negatively correlated with tide height Timing o Present all season o Most abundant June through August o Peak abundance March and April o Most abundant April through June o Peak abundance July o Absent by June o Peak abundance April and May o Presence depends on release dates o Rapid outmigration from natal rivers to estuary

Spatial o High abundance in the Surge Plain, Inner Estuary o High abundance in North Bay and the central o Most abundant in the central estuary. and most notably, the Humptulips River estuary. o Relatively low abundance in South Bay o Low abundance in South Bay, the Hoquiam River and Surge Plain

Unmarked YOY Coho Unmarked Yearling Coho Hatchery yearling Coho

Water Temperature

Salinity o Abundance negatively correlated with salinity o Presence declines rapidly above 5 ‰ o Essentially absent above 20 ‰ Habitat o Presence/abundance positively correlated with: . forested mixed fines/mud channels Tide Height

Timing o Present all season o Present mostly April and May o Present April and May o Peak abundance May o Presence depends on release dates o Peak abundance April Spatial o Most abundant in the Hoquiam River o Most abundant in the Hoquiam River, Humptulips o Virtually absent from the open waters of the river and Charlie Creek Central Estuary, Inner Estuary and North Bay, but abundant in eulittoral marsh; specifically tidal sloughs with some freshwater input

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APPENDIX 5. Water Temperature by Site

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