LOWER CHEHALIS RIVER AND SURGE PLAIN FISH USE …wildfishconservancy.org/projects/lower-chehalis...Grays Harbor (the Chehalis River estuary) is the second largest estuary in the state

LOWER CHEHALIS RIVER AND SURGE PLAIN FISH USE ASSESSMENT

May, 2015

James Fletcher, Todd Sandell and Andrew McAninch

Prepared for: The Rose Foundation

Lower Chehalis River Juvenile Fish Use Assessment, 2015 Wild Fish Conservancy Page 2

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


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


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.


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


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,


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


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.


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).


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,


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:

𝐷𝐷𝐷𝐷𝐷𝐷𝐷 =𝐷𝑡𝐷𝑡𝑡 𝑐𝑡𝐷𝑐ℎ 𝑡𝑜 𝐷𝑠𝐷𝑐𝐷𝐷𝐷 𝑌

𝐷𝑡𝐷𝑡𝑡 𝐷𝐷𝐷 𝑡𝑎𝐷𝑡 ( m2)× 10,000

This is equivalent to the concept of catch per unit 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.


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


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


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


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.


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


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.


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


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).


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).


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


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


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.

Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 24

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


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


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


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

http://wildfishconservancy.org/projects/lower-chehalis-river-and-surge-plain-fish-use-assessment

http://wildfishconservancy.org/projects/lower-chehalis-river-and-surge-plain-fish-use-assessment


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

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

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


APPENDIX 3. Stream Flow

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


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

Unmarked Chinook Hatchery Chinook Unmarked Chum Water Temperature

o Abundance negatively correlated with temp

Salinity Habitat o Abundance negatively correlated with:

intertidal pebble, gravel and sand habitats

o Abundance positively correlated with: 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 April through June o Peak abundance April and May

o Most abundant June through August o Peak abundance July o Presence depends on release dates

o Peak abundance March and April o Absent by June o Rapid outmigration from natal rivers to estuary

Spatial o High abundance in the Surge Plain, Inner Estuary and most notably, the Humptulips River

o Relatively low abundance in South Bay

o High abundance in North Bay and the central estuary.

o Low abundance in South Bay, the Hoquiam River and Surge Plain

o Most abundant in the central estuary.

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 Peak abundance May

o Present April and May o Presence depends on release dates o Peak abundance April

Spatial o Most abundant in the Hoquiam River o Virtually absent from the open waters of the

Central Estuary, Inner Estuary and North Bay, but abundant in eulittoral marsh; specifically tidal sloughs with some freshwater input

o Most abundant in the Hoquiam River, Humptulips river and Charlie Creek


APPENDIX 5. Water Temperature by Site

Documents

LOWER CHEHALIS RIVER AND SURGE PLAIN FISH USE …wildfishconservancy.org/projects/lower-chehalis...Grays Harbor (the Chehalis River estuary) is the second largest estuary in the state