Category Archives: Hatcheries

American River Nimbus Hatchery – Fish Ladder and Public Health Update

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The new fish ladder at the Nimbus Fish Hatchery is coming along.  It will help in hatchery operations and allow salmon and steelhead a bit more spawning habitat because it no longer requires installation of a seasonal weir that keeps fish from migrating to the short stretch of river that is upstream of the hatchery and downstream of Nimbus Dam.

I visited the site on the Saturday after Thanksgiving.  I missed the river in this Covid year.  I thought with the recent limited stay-at-home order the popular viewing area would not be too crowded for a brisk walk with a dog to see the new ladder and a whole lot of salmon.  I was surprised by the crowd, but found a parking spot.  I donned my mask and headed for the viewing area.  Hundreds of viewers with dogs, bikes, and strollers.  There was limited mask wearing and social distancing.  It was actually kind of scary given my many months of minimal human contact.  Having a masters in public health did not give me greater confidence.  I did my best to avoid everyone and follow the recommendations adopted by the Sacramento County Health Department.

I suggest CDFW put up appropriate warning signs and require masks and social distancing at its popular venue.

 

Yuba River Salmon 2020

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In a 2017 post and a 2018 post, I related the status of Yuba River Chinook salmon runs. The 2017 spawning escapement estimate was a record low. The 2018 and 2019 runs were not much better (Figure 1). While the record low 2017 can be blamed predominately on the 2013-2015 drought, the poor 2018 and 2019 runs cannot. Water year 2016 was a normal water year and 2017 was a wet year.

The likely culprit in the decline in Yuba escapement is the continuing persistent decline of wild spawners and increase in hatchery strays (greater than 90% of the run), leading to the erosion of the locally adapted Yuba River salmon population. This was the diagnosis for the overall Feather River population by Willmes et al., 2018.

Figure 1. Yuba River fall run salmon escapement 1953-2019.

A further look at the composition of the hatchery strays in the Yuba escapement surveys provides added clues about the cause of the recent decline in overall escapement to the Yuba River. In 2016 (Figure 2), nearly half the tag returns were strays from the Battle Creek hatchery, while the other half were a combination of spring-run and fall-run strays from the Feather River hatchery, along with a smattering of strays from the hatcheries on the American and Mokelumne rivers. In 2017 (Figure 3), Yuba tag returns featured an even greater proportion of strays from Battle Creek, the American, and the Mokelumne. In 2018 (Figure 4), about half of the tag returns were from the Mokelumne River hatchery, and a third were of Feather River spring-run hatchery origin.

Feather-tagged spring-run show up consistently in the Yuba escapement surveys. This is unusual, because spring-run make up only about 10% of the Feather hatchery smolt production, with fall-run being about 90%. One reason is that spring-run smolts are 100% tagged, while fall-run hatchery smolts are only 25% tagged. Another reason is that all the spring-run smolts are released near Gridley just upstream from the mouth of the Yuba, whereas most of the fall-run smolts are released in the Bay. A third reason is that in most years springtime flows in the Yuba are higher and colder than those in the Feather, and are thus more likely to attract returning adults. Regardless of the reason, the fact that a significant portion of Yuba “fall run” escapement is derived from spring-run hatchery smolts is cause for concern.

Battle Creek hatchery fall-run made up about half the tag returns in 2016 and 2017. Much of the smolt production from the Battle Creek hatchery was trucked to the upper Bay in 2014 and 2015, a strategy prone to increased straying.1 No Battle Creek hatchery smolts were trucked to the Bay in 2016, and none showed in the Yuba in 2018. With over 10 million fall-run smolts produced at the Battle Creek hatchery (federal Coleman Hatchery near Red Bluff), nearly double the Feather hatchery production, it is easy to see why Battle Creek hatchery salmon could dominate the Yuba escapement. Without the Battle Creek, American River, and Mokelumne River hatchery strays in 2017, the record low escapement in the Yuba River would have been far worse. The fact that most of the 2017 spawners were hatchery strays from rivers other than the Feather should also be cause for concern.

In conclusion, the escapement of fall-run salmon to the Yuba River has declined over the past five years, approaching record-low levels. Spawners are now predominately hatchery strays from smolts released in the Bay and along the coast. Natural “wild” Yuba River smolt production is virtually nonexistent. This is a crying shame for what is widely regarded as one of the best non-hatchery salmon rivers in the Central Valley. I have spent many days on the Yuba River over the past two decades. I observed the big runs at the turn of the century and in 2013 and 2014. The river’s pools turned purple with adult salmon. Dead and dying salmon filled the backwaters, feeding eagles and buzzards. The odor was prevalent. Spawning salmon and redds were everywhere. Such occurrences are now rare. Our Yuba River needs so many fixes, a subject for another post.

Figure 2. Composition of tag returns from Yuba River spawners in 2016. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. BCF = Battle Creek fall run. MeRF = Merced River fall run. Data source: rmis.org.

Figure 3. Composition of tag returns from Yuba River spawners in 2017. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. BCF = Battle Creek fall run. Data source: rmis.org.

Figure 4. Composition of tag returns from Yuba River spawners in 2018. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. Data source: rmis.org.

Mokelumne River Hatchery 2017 Releases

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In previous posts over the past two years, I remarked on the progressive management of the Mokelumne River Hatchery, a mitigation hatchery operated by the California Department of Fish and Wildlife in partnership with the East Bay Municipal Utility District. Hatchery production over the past several decades has led to the recovery of Mokelumne River fall-run Chinook salmon (Figure 1 and 2). There were remarkable returns to the Mokelumne in 2017, despite the 2013-2015 drought. Returns from 2016 hatchery releases in 2018 were also good.

The hatchery’s annual 6 million smolt releases in 2017 (Table 1) survived well under the hatchery’s management practices (Figure 1). Returns of adults two years later to the river and hatchery below Camanche Dam in 2019 totaled 10,000 to 20,000 as in other recent years (Figures 1 and 2).

Overall, a good 2019 escapement was expected because 2017 was a wet year. However, in-river numbers (Figure 2) in 2019 were not as high as might be expected.. Hatchery return patterns were similar to those from the 2016 releases returning in 2018. Again, the best returns were from releases of hatchery fish to the coast near the Golden Gate and from Half Moon Bay just south of San Francisco (Figure 3). Returns ranged from near zero to 2.5 percent (Figure 3). The half-million smolts released to the river had near zero returns to fisheries and river/hatchery, while the one million releases to the coast in May had good returns of 1.3 to 2.5 percent. Late May releases (900,000) from the east Bay at Sherman Island also had good returns of 1.5 to 1.8 percent. Earlier May and late April releases to coast, east Bay, and river (nearly 4 million) had returns less than 1 percent.

Since 2017 was a wet year with high spring Delta outflow than drier 2016 (Figure 4), a better return would be expected from the 2017 hatchery releases to the Mokelumne River and even the eastern Bay. The river also had much higher flows in spring 2017 (Figure 5), which should have benefitted in-river hatchery releases. Late May releases proved much more successful in wet year 2017 than late April or early May releases, even to the coast, providing further evidence of better performance of later release of older, larger hatchery smolts. But the continued poor returns from in-river releases even in wet year 2017 remains a problem.

Meanwhile, straying of fish produced in the Mokelumne remains an issue. Up to half or more of returning adults stray to other Central Valley rivers and hatcheries. Maintaining genetic integrity and “wild” spawners in spawning reaches of individual Central Valley rivers would require marking or genetic tests of all hatchery fish, as well as measures to keep hatchery-origin and stray adults from individual spawning grounds. Maintaining genetic integrity and minimal “domestication” of the hatchery stocks would require selective brood stock management in the hatcheries.

Figure 1. Returns to Mokelumne Hatchery 1964-2019.

Figure 2. In-river spawning grounds counts 1952-2019.

Table 1. Summary of Mokelumne Hatchery smolt releases in spring 2017. Source: https://www.rmpc.org

Figure 3. Percent return of 2017 Mokelumne Hatchery tagged smolt releases. Source: https://www.rmpc.org

Figure 4. Delta outflow spring 2016 and 2017.

Figure 5. River flow at Woodbridge Dam 2016-2017.

 

Winter-Run Salmon Update – August 2020

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In my last update, March 2019, I summarized the population trends of winter-run Chinook salmon through 2017. In this post I include run estimates for 2018 and 2019. The trend indicates the population is recovering from the poor runs in 2016 and 2017 (Figures 1and 2), which were the consequence of poor spawning and rearing conditions.

The improvement is the result of more hatchery contributions and better natural contributions. The strong spawner-recruit relationship continues (Figure 3), with an improved 2019 run that spawned (in hatchery and wild) in summer of normal year 2016 and reared and emigrated during wet water year 2017. In contrast, the poor 2016 and 2017 runs were a consequence of critical drought conditions during spawning (2013 and 2014) and rearing/emigration (fall-winter of water years 2014 and 2015). The 2017 run could have been even worse had hatchery smolt releases not been doubled in winter 2015.

NMFS (2019) concluded the recovery was due to increased hatchery contributions and “better water management”. The latter is simply not true. Year 2017 was a wet year that contributed to good fall-winter survival of broodyear 2016 (Figure 4). By December 2019 NMFS knew that its draft biological opinion was being revised to limit protections.1

The prognosis for the 2020 run (from brood year 2017) is good given wet year summer spawning and incubation conditions in 2017 and normal year winter 2018 conditions. With hatchery stocking back to the normal 200,000 annual smolt level in the Sacramento River at Redding, a run of 3000-5000 can reasonably be expected despite the depleted spawning run in 2017. High summer egg-to-fry survival in 2017 (Figure 4) will also contribute. The 2020 run may also benefit from the initial release of 215,000 winter run hatchery smolts into Battle Creek in 2018. Some of these will return as two-year-old “jacks and jills” in 2020.

Several factors make the prognoses for the 2021 and 2022 (and future) runs less optimistic. Egg/fry survival of wild winter-run was lower again in 2018 and 2019 (Figure 4). The new (October 2019) federal Biological Opinion for winter-run is less protective than the Opinion it replaced,2 and the Bureau of Reclamation’s new water management is explicitly directed toward maximizing water deliveries.

On the positive side, hatchery releases including releases into Battle Creek continued in 2019 and 2020, and the estimates of migrating juvenile winter-run were higher for brood year 2019 in wet summer 2019 (Figure 5). As a result of a Settlement Agreement with CSPA, the State Water Board has required the Bureau of Reclamation to develop new protocols to meet water temperature requirements in the Sacramento River. It remains to be seen how these protocols translate into practice.

In the past three decades, the essential needs for winter-run salmon have not been met.3 Management of winter-run salmon must improve survival of wild eggs and juveniles in the summer spawning and fall-winter rearing-emigration seasons, with supplementary hatchery smolt releases as necessary. We cannot simply rely on wet years to keep wild winter-run salmon going in the Sacramento River.

Figure 1. Spawning population estimates of adult winter-run salmon in the upper Sacramento River from 1974 to 2019. Source: CDFW GrandTab and NMFS.

Figure 2. Spawning population estimate since 1997 showing proportion of hatchery and wild adult spawners. Source: NMFS (2019).

Figure 3. Spawners versus recruits (spawners three years later) transformed (logx minus 2). Year is recruit year spawners. For example, 2017 is the run size for 2017, representing spawners from brood year 2014. Color denotes water-year type in fall-winter rearing/emigration year: bold red is critical year, non-bold red is dry year, yellow is below-normal year, and blue is wet year. For example, red 15 and dot margin represent critical water year 2013. Yellow dot fill represents spawning year was a below-normal water year. Note 2016 and 2017 had both critically dry year summer spawning and fall-winter rearing-emigration. The blue 2019 point is a preliminary estimate.

Figure 4. First summer survival rate by brood year based on egg and fry production rate estimates. Egg number is derived from adult spawner estimates. Fry number is derived from Red Bluff screw trap estimates. Source: NMFS.

Figure 5. Brood year winter-run salmon early life history and abundance (2005-2019) as measured at Red Bluff. Source: http://www.cbr.washington.edu/sacramento/tmp/hrt_1599751617_74.html

 

Partnership Shares Science to Find Fish and Water Solutions

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“This month six California and federal agencies representing water management, fish, and wildlife, along with the Sacramento River Settlement Contractors, signed onto the Sacramento River Science Partnership. The Partnership establishes an interagency science collaborative in which members will develop, share and discuss science to inform water management activities and protection of fish in the mainstem Sacramento River.” (8/25/20 News Release)

  •  The seven signatories will foster and advance science to inform sustainable solutions to water management challenges including conflicts between water supply delivery and fish survival.

The time when anyone thought that the problems confronting Central Valley salmon could be solved with more science is long gone. The problems and solutions have not really changed in the 40+ years I have been involved. And the problems are only getting worse. Why is it so hard to address them?

The Problems

As a consequence of rainfall, snowmelt, reservoir storage and release, and water diversions, flows in the Sacramento River, have become so low and erratic that they strand salmon spawning redds and create prolonged high water temperatures in the juvenile rearing and migration reaches of salmon. It is a wonder that there are any wild salmon left. Without hatcheries, there would be few if any salmon in the Central Valley at all.

Spring-Summer Water Temperatures

Spring-summer water temperatures in the lower Sacramento River are bad. They kill salmon and sturgeon, block migrations, lead to poor juvenile salmon growth, early migration, high predation, and cause huge predation problems for young hatchery and wild salmon. The high temperatures exceed state water quality standards and water project permit requirements. Yes, water temperatures were bad during the 2013-2015 critical drought, as might be expected (Figure 1). But they have also been bad in the five normal and wet years (2016-2020) since the drought (Figure 2). The safe level is 65°F, but the standard is set at 68°F, above which stress and higher mortality occurs. 68° is supposed to be an upper limit that should not be exceeded, and in past decades it rarely was. It is now the accepted norm, and even then it is not enforced.

In 2020 (Figure 3) spring water temperatures were detrimental to the upstream migration of endangered winter-run and spring-run salmon, emigrating juvenile fall-run salmon, and larval and juvenile sturgeon. High summer temperatures hinder migration of adult fall-run salmon and are detrimental to survival of winter-run fry, over-summering late-fall-run and fall-run salmon smolts, and rearing juvenile sturgeon.

Fall Drops in Water Levels

Often, usually in October-November, flow releases from Shasta reservoir drop sharply in response to decreasing downstream irrigation demands. The decreases lead to fall-run salmon redd dewatering in the upper river spawning area near Redding and poor habitat and emigration flows for winter-run and late-fall run juvenile salmon.

Stranding

Adult and juvenile salmon are stranded throughout the Sacramento River floodplain after winter-spring, high-flow events. In addition, drops in water surface elevation of four feet in the fall (Figures 4 and 5), soon after spawning de-water the vast majority of fall-run spawning redds in the 20-mile spawning reach downstream of Keswick Dam. Drops in flows after floodway weir spills (Figures 6 and 7) strand adult salmon and sturgeon that are migrating upstream, and also strand juvenile downstream emigrants in the Sutter and Yolo floodway bypasses.

Hatchery Releases

Releases of millions of hatchery-raised salmon and steelhead smolts in winter and spring into the lower Sacramento River from federal and state hatcheries compromise wild salmon and steelhead fry, fingerling, and smolt survival throughout the lower Sacramento River. Hatchery salmon and steelhead prey upon and compete with wild salmon and steelhead, and attract non-native predatory striped bass that also feed on wild salmon and steelhead.

Solutions

A new science plan for the upper reaches of the lower Sacramento River is not going to solve the problems that stem from failure to act on what science has told us for decades.

Solutions to the problems outlined above abound. These solutions are well documented in the Central Valley Salmon and Steelhead Recovery Plan (NMFS 2014) and other stakeholder plans.1 The most important solution, is water temperature limits in the lower Sacramento River, which were adopted decades ago in state water permits and water quality control plans. These limits designed to protect salmon are simply no longer enforced.

Figure 1. Water temperature in the lower Sacramento River from 2013-2015 critical drought years near Grimes, CA. Also shown is average for the past 11 years of record. https://nwis.waterdata.usgs.gov/nwis/

Figure 2. Water temperature in the lower Sacramento River from 2016-2020 post-drought years near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 3. Water temperature in the lower Sacramento River in 2020 near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 4. Sacramento River flows in fall of 2013 below Keswick Dam near Redding.

Figure 5. Sacramento River water surface elevation in fall of 2013 below Keswick Dam.

Figure 6. Spills of water from Sacramento River over Tisdale flood control weir during the period from December 2013 to February 2015. Source: CDEC

Figure 7. Spills of water from Sacramento River over Tisdale flood control weir during the period from January 2016 to May 2017. Source: CDEC