Spawner Abundance and Distribution of Salmon and Steelhead in the Upper Chehalis River, 2019 and Synthesis of 2013-2019

Flood control alternatives being considered as part of the Chehalis Basin Strategy include a Flood Retention Expandable (FRE) facility that would be located in the main stem Chehalis River at river mile 108.2 upstream of the town of Pe Ell. Monitoring efforts in the Chehalis River Basin have not historically focused on delineating population trends above vs. below the location of the proposed facility. However, information on spawner abundance and distribution data in this area of the river was identified as a data gap by the Aquatic Species Enhancement Plan Technical Committee of the Chehalis Basin Strategy (Aquatic Species Enhancement Plan Technical Committee, 2014). This study was undertaken to understand the numbers and species of salmonids that would be affected above, within, and below the area backwatered (referred throughout the document as the inundation footprint) by the proposed FRE facility and its associated temporary reservoir. The This work also informs fish passage needs should an FRE facility be chosen as a structural solution to control flooding within the Chehalis Basin.

Two different frequencies of survey were used to evaluate salmonid spawners above the proposed FRE site – index surveys were conducted at approximately seven-day intervals throughout the spawning period and supplemental surveys were conducted once during peak spawning. Together, index and supplemental surveys covered the entirety of known spawning habitat for each species. Surveys started the third week of September based on prior knowledge of when fish (spring Chinook) begin spawning and continued on a weekly basis through the spawning seasons for spring and fall Chinook salmon, Coho salmon, and winter Steelhead. Surveys concluded in mid-June when no new redds were observed for two consecutive weeks at the end of the project spawning period. An additional survey of the main stem Chehalis River from river mile 108.2 (proposed FRE facility) downstream to the Newaukum River confluence (RM 75.4) was surveyed four times annually, once during the peak spawn timing for each species and run type. The purpose of these additional surveys was to document the spatial distribution of spawning in the main stem river.

Surveys were conducted either on foot, in pontoon-style boats, or by helicopter. Crews identified and recorded all spawning activity by species per reach segment. Individual redd locations were georeferenced. Live and dead fish counts included the species and sex. Carcass sampling included fin mark sampling (adipose fin clip vs. adipose intact), fish length, coded wire tag (CWT) status, and scale collection for aging Chinook and Steelhead. Tissue samples were taken from Coho for genetic analysis.

Results from the 2018-2019 survey season were collected in a similar manner to the previous five survey seasons (2013-2018) to document the spawning distribution of spring and fall Chinook, Coho, and winter Steelhead in the reaches upstream, within, and below the proposed FRE facility footprint and associated temporary reservoir. Major findings from the 2018/2019 survey season include:

• The majority of spawners observed for all species in this area of the watershed were naturalorigin; hatchery fish were rare to absent.
• Abundance of spring and fall Chinook salmon within the study area was estimated to be 3 (spring) and 578 (fall) adult spawners. Chinook spawning activity was observed between September and December. Both spring and fall Chinook spawned primarily in the main stem river, 100% (1/1) and 90% (207/230) of redds, respectively. The percentage of spring Chinook redds found within the FRE facility inundation footprint was 100% (1/1) and fall Chinook 96% (221/230).
• Abundance of Coho salmon within the study area was estimated to be 2,128 adult spawners. Coho spawning activity was observed between late October and February with 25% (270/1062) of redds in the inundation footprint.
• Abundance of winter Steelhead within the study area was estimated to be 956 adult spawners. Steelhead spawning activity was observed between the months of February and June. Percentage of Steelhead redds in the inundation footprint was 33% (194/589).
• On the main stem river from the proposed FRE facility site downstream to Newaukum River, we observed minimal Coho and Steelhead spawning but significant spring and fall Chinook spawning activity. The highest density of fall Chinook occurred between the proposed FRE facility site (RM 108.2) and Elk Creek (RM 100.2). In contrast, spring Chinook spawning distribution was more evenly distributed between the proposed FRE facility site and the Newaukum River.

After six years of intensive monitoring in the Upper Chehalis sub-basin above the proposed FRE facility we found that spawning occurred almost continuously from September through June. The majority of spawning for spring and fall Chinook occurred within the mainstem and inundation footprint. Coho and Steelhead utilize the mainstem habitat in the inundation footprint but a greater proportion of their spawning occurred upstream and in tributaries. There is also a higher density of spawning by spring and fall Chinook in the mainstem below the proposed FRE facility near Pe Ell when compared to other mainstem locations.

During the first four field seasons (2013-2018), Steelhead were the most abundant species utilizing the spawning habitat above the proposed facility. Coho had the next highest abundance followed by fall Chinook and spring Chinook. However, in the last two years of the study (2017-2019) a shift has occurred, and Coho are now exhibiting higher spawner abundances than Steelhead, which have been declining in abundance since 2015. In addition, Coho are exhibiting a brood cycle decrease in abundance every three years that can be traced back to the 2007 flood. Overall, spring Chinook exhibited a ten-fold decline after the first two years of the study. This could be partially attributed to refinement of the method for field identification of spring Chinook to a weight of evidence approach that was formerly implemented during the 2015/2016 survey season. However, there was also a noticeable decline of total spawner abundance in the last week of September and first week of October which indicates that this decline was likely not just due to a refinement of methodology. A way to validate field calls or alternative ways to differentiate spring from fall Chinook spawners needs to be developed. Recent studies on genetics and otoliths holds promise for new and more accurate methods for determining run-type, but there is still work needed to make that information available for field biologists.

The Upper Chehalis sub-basin does not have a large component of hatchery strays for any species but data on the hatchery-origin contribution to the Steelhead run has been uncertain. While snorkel surveys have not confirmed hatchery presence, results from spawning ground surveys revealed two carcasses with adipose fin clips. It is apparent from our data that the convention of using March 15th as a cutoff date for hatchery- to natural-origin Steelhead when estimating escapement is not be appropriate for the Upper Chehalis sub-basin and likely not appropriate for other areas in the Chehalis basin. Compared to other species, Steelhead make up the greatest contribution (15.43%) to the entire Chehalis basin spawner abundance. Other species (spring Chinook, fall Chinook, and Coho) contribute less to the Chehalis basin totals at 1.25%, 3.37% and 2.72%, respectively. Though these proportions may seem small relative to the entire Chehalis Basin, genetic data supports that the Upper Chehalis Coho contribute a sizable abundance to a population that is genetically diverse from the rest of the Chehalis basin. Steelhead in the Chehalis basin also have a population structure that is genetically diverse and is comprised of three distinct groups: Willapa Hills, Cascades, and Olympics. Chinook salmon also show genetic diversity between the upper basin and lower basin populations. Genetic diversity as well as habitat heterogeneity is important to the continuation of these species in the face of climate change and anthropogenic impacts. We do not fully understand the extent to which these genetically distinct populations in the Upper Chehalis sub-basin contribute to the Chehalis population. However, all six years of the study demonstrate that spring and fall Chinook, Coho, and Steelhead actively spawn at varying levels of intensity in the area likely to be impacted by the proposed FRE facility.