Eel River Recovery Project Final Report: Citizen Assisted 2015-2016 Fall Chinook Salmon Monitoring
Prepared for: Eel River Recovery Project
By: Patrick Higgins, ERRP Managing Director & Eric Stockwell, ERRP Fall Chinook Project Coordinator
With Funding From:
Patagonia World Trout Initiative & Salmon Restoration Association
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 i Acknowledgements
The Eel River Recovery Project (ERRP) faced challenging conditions in estimating the 2015- 2016 Eel River fall Chinook salmon run due to extremely low flows in early fall and then very high flows starting in December. ERRP wishes to thank the Wiyot Tribe and Humboldt Redwood Company for once again co-sponsoring the project. The project was made possible by grant funding provided by the Patagonia World Trout Initiative and the Salmon Restoration Association, which sponsors the World’s Largest Salmon BBQ in Fort Bragg.
ERRP was assisted by dozens of volunteers who participated in lower Eel River dive surveys and in tracking fall Chinook migrations and spawning throughout the watershed. Only three dives were carried out from late October to mid-November in the lower river and only in the 12th Street Pool because of shallow depths, profuse algae and the risk of divers contracting swimmer’s itch. When November rains remained sparse, ERRP deployed kayaks for lower main Eel River spawning surveys.
Results from the Van Arsdale Fish Station and aerial and ground surveys of spawning were shared by fisheries biologist Scott Harris of the California Department of Fish and Wildlife (CDFW). Thanks go out to Park Steiner and PG&E (SEC 2016) for sharing spawning data from the upper Eel River and Tomki Creek, although the latter had no fish sightings this year.
The big story on this year’s run was that Chinook salmon became diseased while holding in lower Eel River pools which lead to blindness. ERRP wishes to thank the local press and electronic media for covering this problem including KMUD radio, KAEF TV, KIEM TV, Redwood Times, the Independent, and the Eureka Times Standard. Reporters Will Houston of the Times Standard and Keith Easthouse of the Independent deserve special mention for their in- depth coverage of the salmon project. ERRP worked cooperatively with CDFW to capture diseased fish for analysis, and we wish to thank Alan Renger of the Fortuna Office for his initiative. Professor Esteban Soto of the University of California, Davis rendered important assistance in analyzing the cause of disease and ERRP is also very appreciative of UCD efforts.
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 ii
ERRP Thanks 2015-2016 Volunteers & the Community for Support
David Sopjes Dave Wagner Sal Steinberg Ernie Merrifield Paul Trichilo Bruce Hilbach-Barger Diane Higgins Dane Downing Paul Domanchuk Dennis Halligan Walker Wise Cathy Warren Greg Byers Larry Bruckenstein Graham and Dotti Russell Doug Parkinson Karen & Scott Walsh Jeff Wells Sharon & Dean Edell Dorje Bond Seth Rick Brandi Easter Sunshine Johnston Jason Webster John Evans/Big Bend Lodge Sam Parker Jeff Hedin Brandon Torske Jim Williams Nolan Cahill Stephen Kullman Bernabe Alvirez Tim Nelson Eric Johnston Domenic Belli Mickey Bailey Jason Webster Talia Rose Willie Grover David Bradfield Sage Halvorson Bernabe Alvidrez Sean Croft Nolan Cahill Tyler Grunert Kevin Silver Jesse Barrer Ashley Woodford Barbara Sopjes Kenny Priest Amy Conway Stephanie Sawyer Richard Geinger
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 iii Table of Contents
Cover……………………………………………………………………………………. i Acknowledgements……………………………………………………………………... ii Table of Contents……………………………………………………………………...... iii Executive Summary………………………………………………………………………..1 Background ………………………………………………………………………………..2 Time, Location and Conditions of Surveys………………………………………………2-4 Methods ………………………………………………………………………………….2-5 Lower Eel River Pool Data ……………………………………………………..…2 Dive Surveys……………………………………………………………………….5 Kayak Surveys...... …………………....…………………………………...... 5 Tributary Surveys…………………....…………………………………...... 5 Volunteer Observations…………………………………………………………….5 Van Arsdale Fish Station ……………………………………………………..……5 Results …………………………………………………………………………………5-12 Pool Depths, Temperature, and Dissolved Oxygen ……………………………...5-7 Kayak Surveys of Lower Eel River Pools …………………………………………7 Spawner Surveys from Kayaks………………………………………………….8-10 Tributary Surveys…………………………………………………………………...9 Van Arsdale Fish Station Chinook Salmon Counts……………………………..9-11 Volunteer Observations ..………………………………………………………11-12 Discussion .…………………………………………………………………...... 13-20 Precision of ERRP Run Estimate …………………………………………………13 Lower Eel River Bed Scour and Chinook Egg and Alevin Survival………………13 Tributary Habitat Impairment……………………………………………………...14 Chinook Salmon Disease Outbreak …………………………………………….14-16 Lower Eel and Van Duzen River Habitat Conditions ………………………...16-17 Lower Eel and Van Duzen River Restoration Opportunities……………………16-18 Poaching and Driving Through Redds ………………………………………… 17-19 Chinook Salmon Run Trends 2012-2015.……………………………………… 19-20 Prospects for Rebound in 2016-2017…………………………………………….....19 Conclusion ………………………………………………………………………………….20 Recommendations …………………………………………………………………………..21 References ………………………………………………………………………………22-23
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 iv Executive Summary
ERRP has successfully estimated the Eel River fall Chinook run since 2012, and each year is unique and has different challenges. The 2015-2016 citizen assisted monitoring project was the most difficult, however, because early rains failed and dives were not able to be scheduled, and then rainfall was so high after December 1 that observation of migrating and spawning Chinook salmon were limited for protracted periods.
Despite the El Nino conditions in the ocean that are usually linked to increased precipitation, rains from September through November were extremely sparse. Lower Eel River flows as measured by the U.S. Geologic Survey at Scotia did not exceed 100 cfs until November 11, which limited fish passage and prevented normal fall flushing of algae beds. Algae impairs visibility and harbors swimmers itch organisms. Consequently, dive surveys were restricted to the 12th Street Pool that is deeper and mixed by winds and other pools were surveyed by kayak.
Early run Eel River fall Chinook were restricted to the estuary during late August and early September as flows at Scotia were only just over 30 cfs. ERRP documented movement of fish upstream as far as the 12th Street Pool by September 21 after light rains, but the major influx into lower river pools was with extremely high tides from October 22-24. Hundreds of Chinook salmon sat in shallow, algae infested pools and about 10% of early run fish went blind as a result of a fluke attacking their eyes.
Dives on October 31, November 7 and November 14 estimated that 920, 1000, and 1200 Chinook salmon were holding, respectively, with approximately 25% of the fish comprised of smaller jack salmon. ERRP estimated 5,000 Chinook salmon were holding in the lower Eel River from the 12th Street Pool downstream on November 14. Extensive Chinook salmon spawning in the main Eel River downstream of Dyerville was documented by ERRP from November 11 through December 1.
Before December 1, Chinook salmon access to headwaters was limited with spawning on the main Eel below Dos Rios, the South Fork below Leggett, and the Van Duzen River downstream of Goat Rock Falls. After December 1, flows were adequate for access and spawners were seen in low numbers throughout the basin, including upper Outlet Creek, Ten Mile Creek, the Middle Fork and Black Butte River, and the upper South Fork near Branscomb. Lower South Fork Eel River tributaries showed a late fall Chinook run peak in mid-December. Chinook arrived at the Van Arsdale Fish Station on December 6, and only 102 fish passed upstream to spawn during the entire season. Spawners were noted in Ten Mile Creek and upper Outlet Creek, but none were seen in Tomki Creek (SEC 2016). ERRP once again found that sediment impairment limited spawning use of a number of other Eel River tributaries.
ERRP used historic run timing and professional judgment regarding fish response to flows to arrive at an estimate for the 2015-2016 late run of 5,000-10,000 fish. The total 2015-2016 Eel River fall Chinook run total estimate is 10,000-15,000. The population is showing a declining trend since 2012, but remains above 10,000 fish and at no risk of loss of genetic diversity. High jack counts indicate another strong year class and improved ocean conditions and restricted ocean fisheries may also favor population rebuilding in 2016-2017. However, ERRP has concern about survival of adult Chinook salmon in the lower Eel River due to poor holding habitat, and strongly encourages expeditious restoration to improve conditions.
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 1 Background
ERRP community scoping meetings in September 2011 highlighted concerns about the potential loss of native Eel River fall Chinook salmon. People expressed frustration over the lack of data available from agencies and wanted more information on fish population trends. Since agency budgets are limited and they lack capacity to collect more data on Chinook salmon population trends, ERRP began volunteer dive surveys and basinwide assessment in 2012. These data may be useful in the future in showing success of restoration efforts, if we are able to help rebuild runs into the 21st Century. ERRP monitoring of lower Eel River habitat conditions has highlighted the problem of diminished adult Chinook salmon holding capacity, which we hope will help stimulate restoration actions. ERRP is able to capture information on Chinook salmon because the community is willing to support counts via volunteer participation and also monetarily.
Time, Location and Conditions of Surveys
Although Chinook salmon are known to enter the Eel River estuary in late August, flows were insufficient to allow passage out of the estuary before mid-September rains. The U.S. Geologic Survey Scotia stream flow gage (Figure 1) shows that flows were hovering around 30 cfs prior to September 14 and never exceeded 100 cfs until after November 9. The lack of flushing flows allowed an algae build up in lower Eel River pools (Figure 2) that prevented dive surveys except for in the 12th Street Pool. Shallow riffle crests posed risk of stranding for Chinook salmon and no passage above the 12th Street Pool was possible until early November (Figure 3).
Dives of the 12th Street Pool took place on October 31 (63 cfs), November 7 (83 cfs) and November 14 (155 cfs). Water temperatures cooled from 64 F on October 31 to 56 F on November 14. Chinook had sufficient water to pass upstream out of Fortuna from November 11 to December 1, but not to access to headwaters, and ERRP did kayak surveys of spawning from Dyerville downstream to Fortuna.
Spawner surveys of lower South Fork Eel River tributaries indicated late fall Chinook salmon spawned from early December 2015 to late January 2016, although high flows and turbidity limited when surveys were possible. Upper South Fork Eel River tributaries Jack of Hearts, Elder and Redwood were surveyed on January 6 when water clarity was excellent. SEC (2016) conducted surveys of Tomki Creek and the main Eel below the Potter Valley Project in December and January, but the number of surveys were also limited by high water and turbid conditions. Late season flows were adequate for Chinook to disburse throughout the watershed (Figure 4).
Methods
ERRP collected data on pool depths, holding Chinook salmon and later spawning data from the lower main Eel River below Dyerville. ERRP also conducted spawner surveys of Eel River tributaries in December 2015 and January 2016.
Lower Eel River Pool Data: Pools depths in the lower Eel River were measured prior to dives using sonar on a kayak. Multiple Onset Optic Pro temperature probes were placed in vertical arrays in the 12th Street and Weymouth Bluffs pools. Dissolved oxygen was measured in the Worswick Pool with a Yellow Springs Instrument multi-probe.
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 2 Dives 7.9-8.2 Tides - Major Fish Influx
Chinook Entry
Figure 1. Eel River USGS Scotia flow gauge shows that flows did not exceed 100 cfs until the first week in November.
Figure 2. Mats of algae and floating globs at the top of the Boxcar Pool that obscure visibility and harbor the organism that causes swimmers itch, making conditions unsuitable for dive surveys. Photo by Eric Stockwell. 9/21/15.
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Figure 3. The broad, shallow riffle crest above the 12th Street Pool prevented Chinook salmon migration upstream until flows exceeded 200 cfs on November 9. Photo by Pat Higgins. 08/28/15.
Figure 4. Flow of the Eel River at Scotia rose rapidly beginning in early December and stayed high throughout the late run Chinook salmon spawning season and for the period of downstream migration for juveniles. Data from USGS.
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 4 Dive Surveys: Dive survey methods are used by agencies such as the U.S. Forest Service and the California Department of Fish and Wildlife (Garmin 2012) to count summer steelhead and spring Chinook in other northern California streams. Divers swim in a line through pools maintaining proper spacing so that fish can be counted as they pass the team. If fish mill in front of the team without passing they are not to be counted, and fish passing back downstream are substracted from the count. Team members relay what they are seeing to a score keeper on the bank and the team confers on observations with the score keeper immediately after the dive to arrive at a final estimate. Counts include adult Chinook salmon (>24”), jack salmon (Chinook <24”), coho salmon, adult steelhead (>16”) and half-pounder steelhead (<16”).
Kayak Surveys: Eric Stockwell was able to get useful counts of holding adult salmon by standing in his kayak and wearing polarized sunglasses to cut glare (Figure 5). Estimates of holding Chinook salmon in lower Eel River pools on November 14 were derived from the efforts of three kayak observers. Spawner surveys from November 11 through December 1 below Dyerville usually covered reaches of 6-8 miles and all redds and live fish were noted and GPS locations logged. Redd sizes were estimated and sites were well photo and video documented.
Tributary Surveys: Surveys to gauge use by Chinook salmon for spawning were conducted on foot by walking in the riparian zone or in the stream for reaches up to a mile in length. Lower South Fork Eel River tributaries within Humboldt Redwoods State Park were surveyed in December and January with live fish, carcasses and redds noted. Similar spawner surveys were conducted on reaches of upper South Fork tributaries on January 6, 2016, including Jack of Hearts, Redwood and Elder creeks. Steiner Environmental Consulting (2016) conducted extensive spawner surveys of the main Eel River downstream of the Potter Valley Project and Tomki Creek.
Volunteer Observations: ERRP conducts substantial media outreach and also uses a phone tree to reach interested volunteers who relay information to help document fish migrations and spawning. Dozens of volunteers participated again in 2015-2016, but high flow limited windows of opportunity.
Van Arsdale Fish Station: CDFW traps all Chinook salmon ascending the ladder at Scott Dam. Each fish is identified as an adult male or female or a jack salmon, measured, and fin clipped before being released upstream to spawn in the main Eel River reach within the PVP.
Results
Pool Depths, Temperature, and Dissolved Oxygen: The Weymouth Bluffs Pool upstream of the Van Duzen River was the deepest measured at 19 feet. The 12th Street Pool was a maximum of 14 feet deep, but other pools further downstream were very restricted in depth. The Boxcar Pool had a maximum depth of 9 feet, but maintained depths of 6-9 feet in only about 10% of the pool. The Drake Pool had a small pocket scoured near rip rap of 10 feet in depth, but most of the pool was 3 feet deep and completely choked with vegetation. The Worswick Pool above Fernbridge was a maximum of 4 feet deep and most of the pool was 3 feet deep. The depth of the Creamery Pool downstream of Fernbridge was not measured because it was so filled in with sediment that Chinook salmon could not hold there. Water temperatures were in the stressful range (McCullough 1999) in the lower Eel River as reflected by near surface temperatures of the 12th Street Pool (Figure 6), although pool temperatures at depth were cooler.
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Figure 5. Eric Stockwell stands in his kayak to observe holding adult Chinook salmon in the Worswick Pool. Photo by Pat Higgins. 10/28/15.
Salmonid Stress = >68F
Figure 6. Lower Eel River water temperatures taken near the surface in the 12th Street and Weymouth Bluffs Pools indicate stressful temperatures for salmon and steelhead. Stress reference from McCullough (1999). Data from ERRP.
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Chinook salmon in the Worswick Pool were being afflicted by disease and were going blind. ERRP was concerned that profuse algae might be causing stressful or potentially lethal dissolved oxygen sags when algae respired at night. ERRP was only able to measure dissolved oxygen for several hours on the afternoon of October 26 before volunteers were asked to leave the location. Results show oxygen rising from 8.65 mg/l in the late morning to 11.12 mg/l later in the afternoon which is indicative of a high level photosynthetic activity (Figure 7). It is likely that nocturnal algal respiration was also dipping below 7 mg/l, which is stressful for salmonids (US EPA 1973), but that could not be confirmed.
The flow as of the last dive had increased to 155 cfs and the small team count should be considered conservative. No adult coho salmon were counted by dive teams, but guides indicated that they were being caught in the estuary during the month of October (Kenny Priest, personal communication).
Kayak Surveys of Lower Eel River Pools: Because of poor water quality and visibility in lower Eel River pools in the early season, dives were not appropriate and instead observers stood up in kayaks and counted fish. Only incidental Chinook salmon were seen in lower Eel River pools until high tides occurred in late October. On October 20, 20 Chinook salmon were counted in the Drake Pool and 100 in the Boxcar Pool. In addition to the 1200 Chinook counted by divers on November 14, kayak estimates of holding fish were 300 in the Boxcar Pool, 1000 in the Drake Pool, and 2000 in the Worswick Pool just above Fernbridge. This total of 5000 Chinook salmon is a conservative estimate of the early run, with some fish having passed upstream of Fortuna by November 14. Kayak observations also lead to the discovery that about 10% of holding salmon had opaque eyes, acted as if they were blinded, and became very lethargic (Figure 8). ERRP helped CDFW collect diseased fish on November 11 for analysis and the fish were refrigerated and shipped to UC Davis.
Dissolved Oxygen (mg/l) Worswick Pool 10/26/15 12.00
10.00
8.00
6.00
4.00
2.00
0.00 11:30 AM 11:45 AM 12:00 PM 12:15 PM 12:30 PM 12:45 PM 1:00 PM 1:15 PM
Figure 7. Worswick Pool dissolved oxygen levels measured on October 26, 2015 during mid-day. Data from ERRP.
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Figure 8. Diseased Chinook salmon captured by ERRP and CDFW on November 11, 2016 showing inflammation of the eyes. Photo by Eric Stockwell.
Spawner Surveys from Kayaks: Table 1 shows the dates of kayak surveys of lower Eel River Chinook salmon spawning and the reaches surveyed. Few Chinook salmon were moving above the Van Duzen River on the first kayak survey on November 11 and those doing so were highly vulnerable to predation and stranding due to low flows (Figure 9). Spawning was active beginning on November 18 in the Dyerville to Holmes reach, but spawning activity had more than doubled ten days later. A total of over 200 redds were counted on the lower Eel River below Dyerville and redd locations were mapped (Figure 10). ERRP also noted significant poaching activity and places where people were driving through redds (see Discussion).
Table 1. Main Eel River Spawning Surveys. Date Reach November 11, 2016 Scotia to East Ferry Road November 18, 2016 Dyverville to Holmes November 19, 2016 Holmes to Stafford November 22, 2016 Dyverville to Holmes November 26, 2016 Twin Creek to Rio Dell November 28, 2016 Holmes to Stafford November 30, 2016 Stafford to Twin Creek December 1, 2016 Rio Dell to Howe Creek
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Figure 9. Chinook salmon migrating in very shallow water above the Van Duzen River on November 11, 2015. Photo by Eric Stockwell.
Tributary Surveys: Bull Creek and its tributaries had far too little flow for Chinook salmon entry until the rains of early December, but eleven surveys were conducted thereafter. Nine adult Chinook were counted on four redds on lower Bull Creek on December 4. December 10 is the first day that adult Chinook salmon could enter smaller tributaries like Canoe Creek and Squaw Creek. Tributary spawning peaked out on December 15 and 16 in Squaw Creek with 24 and 20 Chinook salmon engaged in spawning activity. New spawners, but fewer fish were seen on December 28 and there was even a fresh spawner during the last survey on January 31, 2016. SEC (2016) found low numbers of spawning Chinook in the Eel River Cape Horn Dam and proximate to the mouth of Tomki Creek. However, no live fish carcasses or redds were found in Tomki Creek during surveys. in December 2015 and January 2016. An ERRP survey on January 6 of upper South Fork tributaries found no live fish, carcasses or redds in Jack of Hearts and Redwood creeks. Chinook and coho likely spawned before the upper South Fork surveys, but high flows moved stream cobble and gravel and obscured redd locations. An adult winter steelhead was seen in Elder Creek, which is too small for Chinook salmon use and too steep for coho salmon spawning.
Van Arsdale Fish Station Counts: The first Chinook salmon entered the VAFS on December 5, 2015 because low flows prior to the date had not induced migration. A total of 102 Chinook salmon passed upstream by late December, with 75 adult males, 25 adult females and 6 jack salmon. This count is one of the lowest in recent years (Figure 11), but not surprising given the lack of rainfall and insufficient flow for upstream passage earlier in the season.
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Figure 10. Lower Eel River map of fall 2015 spawning areas as well as places where poaching was evident and where people were driving through redds.
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Figure 11. Van Arsdale Fish Station returns from 1946-2015 show that returns have diminished since 2012, but lack of flow may be as important in shaping the trend as level of escapement. Data from CDFW.
Volunteer Observations: Early season observations by volunteer David Wagner in the lower Eel River were that Chinook were moving up into the Fulmore Pool, but could go no further before mid-September rains. The inability to move upstream into pools made them vulnerable to seal predation, and seal activity in the Fulmore Pool was high. Summer steelhead and half pounders were noted in lower Eel River pools in late September, but fewer than in previous years.
Seth Rick and other volunteers reported on Chinook movement and spawning in the lower Eel River in late November. Graham and Dotti Russell reported movement of a school of Chinook on the South Fork in Phillipsville in the same time period and Talia Rose photographed fish migrating past Piercy (Figure 12). However, these early fish were restricted in migration and spawned downstream of Leggett and none reached Big Bend Lodge upstream of there where John Evans often sees spawning. Scott Harris of CDFW flew in a small plane to observe fall Chinook migration and spawning in the main Eel River in Mendocino County and found no fish upstream of Outlet Creek prior to December 1. Spawning was taking place downstream of Dos Rios and ERRP received confirmation from volunteer Mickey Bailey at the mouth of Woodman Creek where signs of bear predation were evident (Figure 13). Although high flows in December and January limited opportunities to observe migrating and spawning Chinook salmon, ERRP volunteers were able to confirm widespread Chinook salmon distribution and spawning. Low numbers of late run Chinook salmon spawners were seen in the upper South Fork near Branscomb (Sharon Edell), in upper Ten Mile Creek (Evan Engber), in the Van Duzen River above Swimmers Delight (Paul Domanchuk), in the Middle Fork upstream as far as Williams Creek and into the Black Butte River (Bruce Hilbach- Barger). Scott Harris (CDFW) also noted a few Chinook salmon spawning in tributaries of Outlet Creek above Willits, although at very low densities.
Coho salmon were seen migrating into Dutch Charlie Creek in mid-December (Stephanie Sawyer) and spawning in Anderson Creek, tributary of Indian Creek (Richard Geinger) in January 2016.
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Figure 12. Fall Chinook salmon passing upstream on the South Fork near Piercy under very low flow conditions. Photo by Talia Rose.
Figure 13. Freshly killed female Chinook salmon upstream of the mouth of Woodman Creek that was taken by a large black bear from a spawning riffle. Photo by Mickey Bailey. 11/20/15.
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 12 Discussion
The 2015-2016 Eel River fall Chinook assessment was another learning experience as we were able to cope with bad water quality that thwarted dives and high flows that made migration and spawning observations challenging, and were still able to arrive at a useful estimate of the run.
Precision of ERRP Run Estimate: ERRP recognizes that run estimates are not precise, but order of magnitude estimates of the Eel River fall Chinook salmon population are still useful for trend monitoring. Some estimates of lower Eel River pools in November 2015 were made from kayaks because low flows and poor water quality prevented dives. Although somewhat less precise than dives, the estimate of 5,000 fish on November 14, 2015 based on kayak observations and dive results is conservative, especially since some Chinook had already begun migrating.
The 5,000 to 10,000 fish estimate for the latter half of the Chinook run is also conservative, based on the following reasoning. Gibbs (1964) summarized Benbow Dam fish ladder Chinook salmon counts from 1953 to 1963 and documented that half of the Chinook salmon passed before December 1 and half afterward (Figure 14). Since there has been very little hatchery operation on the Eel River and no change in genetics of fall Chinook, it is assumed that run timing in 2015-2016 would be similar. Gibbs (1964) also documented Chinook salmon passage at Benbow Dam as late as March and April, and fish are likely to delay migration and river entry when flow conditions are very low. ERRP (Higgins 2014) documented fresh Chinook salmon still holding in the lower Eel River in Fortuna in January 2014. Near record lows in the lower Eel River in October and November 2015, likely stalled salmon entry making the second half of the run stronger.
Lower Eel River Bed Scour and Chinook Egg and Alevin Survival: Chinook salmon spawning before December 1 was concentrated in the lower Eel River. Flows at Scotia approached or exceeded 100,000 cfs three times in the winter of 2015-2016 and a peak of 174,000 cfs was measured by USGS on January 18, 2016; therefore; it is possible that survival of eggs and fry were low. However, many sites selected by Chinook salmon in the lower Eel River are at locations where the terrace is wide and unconstrained. The energy of the river at these locations is somewhat dissipated on the flood plain, which would reduce shear stress that causes bedload mobility. Survival of Chinook juveniles hatched from main Eel River redds was likely high in 2013-2014, as indicated by the high proportion of jack salmon returns in 2014-2015 (Higgins 2015), but flows never exceeded 80,000 CFS that year. Further study of bedload movement is needed to understand mainstem Chinook salmon spawning success in the lower Eel River in years with high flow.
Van Arsdale Fish Station Returns: The total number of Chinook salmon passing the VAFS in 2015- 2016 was small because the rains and associated increases in flow came late. Chinook salmon spawning habitat in the main Eel River downstream below the Potter Valley Project is of high quality, so passage, and survival of eggs and juveniles may be higher there than if the adults spawned between the dams. The encroaching riparian willow due to the altered flow regime below the dam constricts the channel and disconnects it from the river floodplain. Trinity River studies show that juvenile Chinook salmon survival can be improved if selective areas of riparian are removed to allow movement to slower edge-waters for refuge during high flows. Strategic riparian removal also allows spawning gravel from terraces to become available for spawning substrate.
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Figure 14. Benbow Dam Chinook salmon counts from 1953 to 1963 indicate that approximately half of the Chinook salmon passing came before December 1 and half afterward.
Tributary Habitat Impairment: ERRP (Higgins 2014, 2015) has recognized a pattern where Chinook salmon spawners are avoiding creeks with major sediment over-supply. Salmon Creek in southern Humboldt County and Tomki Creek are not supporting Chinook salmon, which indicates major ecological disruption. Ten Mile Creek and Outlet Creek both still support Chinook salmon, but both are showing signs of stress, including excess sediment transport and flow depletion. Both the latter creeks are losing their ability to produce coho salmon, but have not passed the tipping point in terms of supporting Chinook. Lower Eel and lower Van Duzen River tributaries have been sediment over- supplied, but high flows during the past winter and spring help rejuvenate habitat. For example, sediment stored in lower Bear Creek was flushed into the main Eel River and pools capable of supporting old age steelhead juveniles reformed. Sediment problems also make South Fork Eel River tributaries from Redway to Myers Flat unsuitable for Chinook spawning (Figure 15).
Chinook Salmon Disease Outbreak: Dr. Esteban Soto (2016) of the University of California at Davis analyzed the diseased fish provided by CDFW with the assistance of ERRP. Excerpts from his results follow:
“Opacity of the lens consistent with cataracts associated with digenetic trematodes (eye flukes) encysted metacercaria were observed. Trematodes or flukes are small parasitic flatworms that use vertebrates as their definitive host, and mollusks (usually snails) as their intermediate host.
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Figure 15. Highly turbid waters of Oman Creek with recently deposited terrace of fine sediment that would smother eggs and prevent emergence of alevin or larvae. Photo by Pat Higgins. 1/4/16.
Petechial hemorrhages were observed in the central nervous system, specifically in the brain (optic lobes, cerebellum) and spinal cord. Indication of viral infection of the brain with more analysis still being conducted.”
Although flatworm flukes attacking salmon eyes is not unknown, an outbreak of this proportion had not previously been documented. The flatworm has a complex life history and its free-swimming metacercaria life stage attacked the eyes of Chinook salmon, boring into the eye ball. Mature flatworms formed from the metacercaria within the eye and then laid eggs. The eggs would then have been released into the water column as the salmon carcass broke down or a seagull or other avian scavenger fed on the carcass and passed the eggs in feces back into the water. Eggs hatch into a second, swimming larval form the miracidia, which seeks out a snail as an intermediate host and transforms there to the metacercaria. ERRP has noted a proliferation of Radix auricularia (Figure 16), a non-native snail that could play a role in making parasitic flatworms more abundant.
Brain hemorrhages may be a side effect of the eye infection, as infestation of the eye caused pressure build up within the fish’s brain. UC Davis is studying the virus more extensively, but it may also be secondary to the eye infection. Viral susceptibility could have been increased as the parasitized salmon’s defense mechanisms were overwhelmed as it tried to cope with the flatworm infestation.
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Figure16 . Invasive snail Radix auricularia(above) is extremely abundant in lower Eel River pools (left).
Lower Eel and Van Duzen River Habitat Conditions: The Eel River was 40-50 feet deep prior to the 1964 flood, so the pools that fall Chinook are currently forced to hold in are far from their normal historic range of variability. Historically Chinook could swim from the estuary into cold deep pools during August, where they could take refuge from seals and await fall rains. With the cold stratified layers at depth in the pools and low light conditions, fish could hold without stress for months.
Today early run Eel River fall Chinook salmon sit in pools with warm water that are less than four feet deep. Accustomed to the dark of the ocean depths, the bright light conditions during periods of holding in shallow pools are highly stressful for fish. Fish are constantly harassed by predators and disturbed by sport anglers diurnally before October 1 low flow closures, and nocturnally by poachers who frequent the lower Eel River when fish are trapped. Algal growth in shallow pools is also profuse, and nocturnal dissolved oxygen sags could further add to fish stress and ERRP is concerned about mass mortality, if thousands of fish congregated. The Worswick Pool just above Fernbridge is filling due to bank erosion that is also causing the loss of valuable top soil (Figure 17). Shallow riffles that form in the lower Eel River, especially during prolonged drought, also pose a major threat of salmon stranding. The lower Van Duzen River at its mouth poses the greatest chronic risk, and CDFW has the gravel operator create a barrier until flows increase to 100 cfs at the Bridgeville Van Duzen River USGS gauge (Figure 18).
Lower Eel and Van Duzen River Restoration Opportunities: There is a critical need for immediate action to improve adult Chinook holding habitat in the lower Eel River because the population is likely to continue to increase and fall rains are likely to be sporadic as a result of climate change. Bioengineering could be used to stabilize the failing 4700 foot long cut-bank at the Worswick Pool. Bioengineering uses extensive amounts of live willow that are interbedded with strategic amounts of large rock.
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Figure 17. Unstable river bank on Miranda property at the Worswick Pool from the river bed on receding Eel River flow (at left) and looking upstream during a high flow event with the bank actively eroding (at right).
Boulder deflectors integrated into the project would create scour that increases pool depth and large wood could be embedded to increase cover and habitat complexity. This technique has been successfully used on the lower Mad River (Figure 19). Creating a deeper Worswick Pool will allow stratification, dampen ambient light for holding fish, and likely decrease algae growth. This may reduce the risk of disease infection as the volume of the pool increases, DO fluctuations associated with algae blooms decrease, and snails that graze on the algae and serve as an intermediate host for parasitic flatworms decline.
Figure 18. Gravel dam at the convergence of the Van Duzen River with the lower Eel River that is constructed annually to prevent stranding of adult Chinook salmon until the flows reach 100 cfs at the USGS Bridgeville gauge.
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 17
Figure 19. Failing bank in the lower Mad River near School Road before bioengineering (at left) and after project completion (right). Photos courtesy of BioEngineering Associates.
The lower Van Duzen River also needs to be restored using bioengineering to stabilize the channel and allow pools to form (Figure 20). Willow baffles built perpendicularly to the channel can help rebuild the flood terrace of the lower reaches of the river below Yager Creek and deep planted cottonwoods could help recreate a gallery forest. Building the flood terrace will help focus the energy of the Van Duzen River, accelerate sediment transport, and help channel recovery. As the flood terrace is re-established, pools capable of holding adult Chinook salmon will be created and the channel will be narrower and perennially connected to the Eel River, allowing free migration of fall Chinook salmon. The toe of landslides on the southern bank of the Van Duzen River may need buttressing to prevent mass movement as the current is deflected by the newly re-established floodplain.
Poaching and Driving Through Redds: ERRP was informed of and saw evidence of widespread, systematic poaching at a significant scale in the lower Eel River. The harm done by poaching is both direct – the take of fish, but also indirect as it causes stress that can cause decreased fecundity and even delayed mortality. The homeless encampment at the Boxcar Pool is a chronic problem area and it is located in publicly owned North Coast Railroad Authority property. Similar to the low water year of 2013-2014, ERRP once again found that people are driving their cars as a recreational activity through salmon redds (Figure 21). This latter included the High Rock area within Humboldt Redwoods State Park.
Chinook Salmon Run Trends 2012-2015: ERRP data collected since 2012 (Higgins 2013, 2014, 2015) show that the Eel River fall Chinook salmon population has remained above 10,000 fish (Figure 22). This is well above the number of fish needed to maintain biological diversity, which means that extinction risk is low and basin residents can be assured that extinction is low, but the Chinook salmon population trend since 2012 is down.
Prospects for Rebound in 2016-2017: Several factors favor an Eel River Chinook salmon population bebound: strong year previous year classes (2013-2014 and 2014-2015), high survival the 2015- 2016 brood due to ample winter and spring flows, reversal of recent poor ocean productivity and reduced salmon fishing in the ocean due to the predicted scarcity of Klamath River fall Chinook. The latter will reduce harvest of Eel River fish and should favor increased escapement in 2016- 2017. An improvement in ocean feeding conditions is expected as El Nino gives way to a La Nina.
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Figure 20. Lower Van Duzen River wide flood plain with areas that willow baffles and deep planted cottonwoods could be used to rebuild the flood terrace, help focus the rivers energy and to create a more defined channel.
Figure 21. ERRP lower Eel River Chinook salmon spawning surveys found evidence of people driving through salmon nests at several locations, including at Shively above. Photo by Eric Stockwell.
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Figure 22. ERRP fall Chinook escapement estimates from 2012-2013 to 2015-2016 showing a declining trend.
Conclusion
ERRP will continue to provide Eel River fall Chinook salmon trend data to the community to help keep tabs on the population level and to try to enocourage restoration efforts. The declining trend from 2012 to 2015 is concerning, but somewhat expected given the poor ocean productivity over the last several years. The population is still sufficiently large and well distributed that there is no immenent risk of extincition, but ERRP wants to seek basinwide cooperation to rebuild the run to 100,000 in the 21st Century. Going forward there are challenges from climate change in the form of chronic droughts, potential damaging floods, and oscillating ocean productivity. Stream beds are rejuvenated and highly suitable for Chinook salmon spawning in two thirds of the Eel River basin, having recovered from the 1964 flood. At the same time, other major salmon spawning streams are being shut off by a new wave of sediment pollution and stream dessication. ERRP will continue work with rural land owners, including cannabis farmers, to conserve water and prevent erosion and pollution so that these tributaries may once again support salmon in the future. ERRP will work with agencies, Tribes, other non-profit organizations, and private land owners to promote expeditious restoration of the most critical habitat areas. The experience of the 2015-2016 monitoring season also suggests a need for more education and community organizing to better protect the fish from poaching and from people driving through their redds.
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 20 Recommendations
Continue to refine dive formations that induce least stress on fish; increase use of GoPro cameras to count fish and document movement; and add use of a drone equipped with a camera for census of shallow lower Eel River pools. Encourage collaboration with CDFW to strategically use dual frequency sonar technology (DIDSON) to better quantify Eel River fall Chinook. Explore options for measuring lower Eel River redd stability and viability using scour chains and pursue resources and partners to carry out studies. Support project on the lower Eel River to stabilize eroding bank in Worswick Pool above Fernbridge to create a deeper, stratified pool that could hold adult Chinook salmon even in drought years. Promote Eel River Salmon Parkway that replaces homeless encampment with trail and parks along the NCRA right of way. Restore lower Van Duzen River below Yager Creek using bioengineering to bring back perennial surface flows, reduce the risk of stranding, and scour pools for adult and juvenile salmonid use. Promote restoration of the Eel River reach within the Potter Valley Project using techniques similar to the successful Trinity River Restoration Program feather edging projects (Hoopa Valley Tribe Fisheries Department, et al. 2011). Promote discussion of potential large wood projects to accelerate recovery of lower Eel River and Van Duzen River tributaries from sediment impacts. Work closely with CDFW to monitor the lower Eel River for signs of fish disease outbreaks. Map lower Eel River pool depths and monitor for temperature to gauge suitability for holding adult Chinook salmon. Measure dissolved oxygen in Worswick Pool in September-October 2016. Conduct a lower Van Duzen River habitat survey to map low water holding areas and to explore potential locations posing risk for fish stranding. Work with California State Parks on issue of High Rock redd driving. Work more closely with CDFW on to help reduce poaching. Continue to work on sediment, tributary flow and water quality issues to improve overall ecological condition of the Eel River
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 21 References
Garman, C. 2012. Amended 2012 Butte Creek Spring-run Chinook Snorkel Escapement Survey. Memo from environmental Specialist Clint Garman to Joe Johnson, Senior Environmental Specialist. California Department of Fish and Wildlife, Chico, CA. 5 p.
Gibbs, E. 1964. Letter from CDFG Fisheries Biologist Earl Gibbs to CDFG Fisheries Management Supervisor Elton Bailey, re: Benbow Dam, Fish Passage. Dated March 13, 1964. CDFG, Sacramento, CA. 4 p.
Higgins, P.T. 2013. Final Report: 2012 Lower Eel River Volunteer Fall Chinook Dive Census. Published January 31, 2013. Performed under contract to the Trees Foundation for the Eel River Recovery Project with funding from Patagonia and Rose Foundation. ERRP, Arcata, CA. 37 p. http://www.eelriverrecovery.org/doc/ERRP_Higgins_Chinook_Dives_2012_Final.pdf
Higgins, P.T. 2014. Final Report - Eel River Recovery Project Eel River Basin 2013-2014 Fall Chinook Salmon Monitoring. Performed under contract to the Trees Foundation for the Eel River Recovery Project with funding from Patagonia and the Salmon Restoration Association, and the Humboldt and Mendocino Redwood Companies. ERRP, Arcata, CA. 43 p.
Higgins, P.T. 2015. Eel River Recovery Project Fall Chinook Salmon 2014-2015 Citizen Monitoring. Performed under contract to the Trees Foundation for the Eel River Recovery Project with funding from Patagonia, the Salmon Restoration Association, and the Humboldt and Mendocino Redwood Companies. ERRP, Arcata, CA. 25 p. www.eelriverrecovery.org/documents/ERRP_FCH_2014_2015_Final_Rpt_05_26_15_EDITED.pdf
Hoopa Valley Tribe Fisheries Department), McBain & Trush Inc., and Northern Hydrology & Engineering. 2011. Channel rehabilitation design guidelines for the mainstem Trinity River. Prepared for the Trinity River Restoration Program, Weaverville, California. HVTFD, Hoopa, CA.
McCullough, D. 1999 . A Review and Synthesis of Effects of Alterations to the Water Temperature Regime on Freshwater Life Stages of Salmonids, with Special Reference to Chinook Salmon. Columbia Intertribal Fisheries Commission, Portland, OR. Prepared for the U.S. Environmental Protection Agency Region 10. Published as EPA 910-R-99-010.
Soto, E. 2016. Eel River Chinook Salmon (Oncorhynchus tshawytscha) Parasitic-•‐Viral Co‐infection. Prepared by Dr. Esteban Soto, University of California Davis for the California Department of Fish and Wildlife. Department of Medicine & Epidemiology, School of Veterinary Medicine, Davis, CA. 4 p.
Steiner Environmental Consulting. 2016. Upper Eel River Salmon Surveys and Ladder Count 2015-2016 (WY 2016). Performed under contract to Pacific Gas and Electric Company by Steiner Environmental Consulting, Ukiah, CA. 7 p.
United States Environmental Protection Agency (EPA). 1973. Development of Dissolved Oxygen Criteria for Freshwater Fish. Ecological Research Series EPA-R3-73-019. February.
Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 22 U.S. Fish and Wildlife Service. 1960. Survey of Chinook salmon spawning habitat in northwestern California. Natural Resources of Northern California Report, US Fish and Wildlife Service, Pacific Southwest Field Committee, Sacramento, CA. 104 p.
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