Category Archives: Chinook Salmon

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.

 

The Delta as Salmon Nursery

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The Delta is an important nursery area for Central Valley Salmon. This fact continues to be ignored or under-appreciated. The phenomenon is fully consistent with the general science on salmon in their southern range in the eastern Pacific. Nearly all California Chinook salmon are “ocean-type,” meaning that juveniles reach the ocean in their first six months after rearing for extended periods in estuaries. To grow, young salmon fry need to rear in winter in warm productive areas of floodplains and tidal estuaries (Bay and Delta). Flood control infrastructure limits floodplain habitat except in wetter years. Water management, mainly reservoir storage, limits transport of fry to the Bay except in wetter years.

That leaves the Delta as the key nursery area in non-wet years. Thus, the state of the Delta in non-wet years largely determines the success of Central Valley salmon. Salmon smolt production to the ocean is one to several orders of magnitude lower in drier years, which is the fundamental cause of salmon run declines over the past several decades during periods of drought (Figure 1).

Getting salmon fry to the Delta, successfully rearing them in the Delta, and then getting them to the Bay and Ocean are keys to their success. Peaks between droughts, and even small runs during droughts, are driven by trucking smolts from the hatcheries to the Bay and Ocean, bypassing the Delta survival sink. Without hatchery contributions, the underlying pattern for wild-natural salmon would show drastic declines during and after droughts. Improving Delta-derived smolt production is the key to improving the wild component of Central Valley salmon.

For nearly four decades, I have been promoting Delta salmon habitat improvements.1 I have also helped show the importance of winter rearing of salmon fry in the Delta.2 I have also conducted a comprehensive review of Delta salmon rearing habitats and restoration.3 In other posts in this blog, I have offered much discussion on the role of the Delta in salmon production and survival.

The State Water Resources Control Board is in a multi-year process of updating decades-old water quality standards. Focusing on salmon as a key public trust resource is the way to go. The new standards need to assure that fry get to the Delta, do well in the Delta, and then get to and through the Bay to the Ocean.

Figure 1. Over the past several decades the Central Valley fall-run Chinook salmon has declined sharply during and shortly after three major periods of drought: 1987-1992, 2007-2009, and 2013-2016. Source: CDFW Grandtab.

 

  1. Cannon , T. C. 1982. The importance of the Sacramento-San Joaquin estuary as a nursery area of young Chinook salmon. Unpublished NMFS report. ↩
  2. http://www.fisheryfoundation.org/Reports/2005-2006%20Western%20Delta%20seine%20survey%20report.pdf ↩
  3. https://calsport.org/news/wp-content/uploads/Overview-Habitat-Restoration-in-Delta-LowRes.pdf ↩

Feather River Fall-Run Salmon Update – 2019 Spawning Run

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Feather River spring-run and fall-run salmon are the backbone of the California salmon fisheries, making up 20-40% of the total catch and spawning runs. In a review of Feather River fall-run Chinook salmon in September 2019, I described their status through the 2018 run and expressed optimism for the 2019 run. My assessment proved overly optimistic, as the 2019 run numbers came in lower than expected. The lower-than-expected returns appear to be the consequence of the 2017 Oroville Dam spillway failures.

The 2019 spawning run (escapement), though improved over the previous four drought-influenced years, was smaller than those of the previous wet-year-influenced periods 2000-2002 and 2012-2014 (Figures 1 and 2). The run of 80,000 adult salmon in 2019 should have been 25-50% higher, because 2017 was a wet year. The 2019 run, the offspring of brood-year 2016 was raised in the river and hatchery in winter 2017 during the events of the February 2017 spillway failures (Figure 3). The 2019 run showed lower hatchery and wild river smolt production due to the the direct and indirect consequences of the spillway failures. Suspended sediment (turbidity) levels during the spillway failures in the river and the hatchery reached highly stressful if not lethal levels (Figures 4 and 5). These levels were elevated through the winter and spring of 2017 due to the dredging of spillway debris from the river immediately below the failed spillway (Figure 6). Lower Feather River flows during the winter and spring were highly erratic (Figure 7) due to efforts to repair the spillway and dredge the debris from the river below the spillway. Rapid flow reductions from the dam led to well-documented stranding of young salmon in the lower Feather River floodplain.1

The prognosis for the 2020 run is mixed. Spawner numbers in 2017 were fair (80,000; Figure 1). Water year 2018 was below-normal, generally leading to poor spawning, rearing, and emigration survival. Hatchery smolt releases in 2018 were increased several million over 2017 releases, which should bode well for the 2020 run. Wild spawning and rearing in fall of 2017 and winter-spring of 2018 still had to contend with the ramifications of the 2017 spillway failures, although some restoration did occur in summer 2017.2

Figure 1. Feather River fall run Chinook salmon escapement (river and hatchery counts 1964-2019.

Figure 2. Feather River Fall-Run Chinook salmon spawner-recruit relationship. Recruits are escapement for that year. Spawners are recruits from three years earlier. Red represents drought conditions during brood year rearing. For example: 2015 represents winter-spring of 2015 when brood year 2014 was rearing and migrating in lower Feather River downstream to the Bay. Blue designates wet year rearing and migrating conditions. Green represents normal years. Note 2017 represents the 2019 escapement from young reared and emigrated in winter-spring conditions in 2017, a wet year.

Figure 3. Oroville Dam main spillway failure in February 2017. Oroville Dam was constructed during 1961-68 period.


Figure 4. Turbidity (NTUs) measured below spillway in lower Feather River in Oroville, February 9-10, 2017.

Figure 5. Photo of emergency spillway use on February 11, 2017.

Figure 6. Turbidity measured in Feather River near spillway recovery efforts in winter 2017. Spikes in turbidity occurred during ongoing dredging and debris removal activities.


Figure 7. Streamflows in lower Feather River at Gridley and lower Sacramento River below mouth of Feather River at Verona, and turbidity at Verona in winter-spring 2017. CDEC data.

  1. White, J.S.S., K. Lentz, and J. Kindopp. 2017. Stranding of Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (Oncorhynchus mykiss) in the lower Feather River, 2017. Final Report. Department of Water Resources, Division of Environmental Services, Oroville, CA. ↩
  2. https://youtu.be/UcAFs3c4tlA , https://youtu.be/hqeN5-qzlDQ ↩

Limiting Harvest Won’t Rebuild Salmon Run

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The federal-state Salmon Rebuilding Plan for Sacramento River Fall Chinook (SRFC) (July 2019)1 was developed by the Pacific Fishery Management Council (PFMC) under a grant from the National Marine Fisheries Service (NMFS). The plan was developed because the SRFC escapement (in-river and hatchery return spawners) for brood years 2012-2014 declined significantly after the 2013-2015 drought, as shown in counts of adults that returned in 2015-2017 (Figure 1).

Regrettably, this plan is doomed to failure in periods of drought, because it does not address the underlying problems or long-term solutions that would contribute to meeting goals in the future. As stated in the plan, “the occurrence of reduced stock size or spawner escapements, depending on the magnitude of the short-fall, could signal the beginning of a critical downward trend.” This is the problem any salmon rebuilding plan must correct.

Instead, the plan focuses on three strategies as alternatives: no action, reducing harvest quotas by 30%, and closing regional elements of fisheries (including all inland river fisheries). The plan’s focus on reducing harvest or increasing hatchery production will not address the population crashes during multiyear droughts and limited recovery in subsequent normal and wet years that are the main underlying cause of the population’s decline.

The plan was prepared by the Salmon Technical Team, NMFS, and Council staff with support from state and federal agencies and tribal scientists. The plan is based on an extensive review of all aspects of the issue by many knowledgeable salmon scientists. The goal is to create a consensus plan for how the SRFC stock should be rebuilt so it can sustain a maximum yield harvest strategy within several years.

The plan is designed to meet specific goals and objectives. The goal is to rebuild the SRFC stock so it can provide a Maximum Sustained Yield (MSY) of 122,000 hatchery and natural-area adults to coastal and in-river fisheries. This goal has been in place since 1984. The objective is to reach the goal in two to three years.

The Salmon Rebuilding Plan is not a plan to protect and recover the Evolutionary Significant Unit designated as Central Valley Fall-Run Chinook Salmon and its component subpopulations of wild, naturally produced salmon in the river and its tributaries. Instead, it is a plan to rebuild stocks for harvest and escapement including hatchery and “wild” salmon. The plan’s strategy focuses on adjusting the fishery efforts and harvest to accomplish the PFMC’s goal of rebuilding the fishable stocks, factors the PFMC can control, while mentioning the real problems and other, more long-term solutions in passing.

The plan summarizes the development team’s analyses and conclusions, and suggests multiple factors contributed to the escapement decline of SRFC in years 2015-2017.

The critical broods of 2012-2014 resulted in well below average ocean abundance index values and adult spawner escapement in 2015-2017. Brood year 2014 appears to be the weakest of the critical broods as it was the primary contributor to the very low 2017 SI postseason estimate and one of the lowest spawner escapement estimates on record. The record low escapement to the upper Sacramento Basin in 2017 is particularly noteworthy. ( p. 60)

Some of the statements in the plan, and my response to each, are shown below. They are organized by topic.

1. Early Life History Survival –

The analysis found that below average freshwater flows and high temperatures throughout the Sacramento Basin coincided with relatively high levels of pre-spawn mortality for the critical broods (defined as brood years 2012-2014). Low flows and warm temperatures in the lower Sacramento River were likely to have affected survival of outmigrating smolts from brood years 2013 and 2014….. The 2013-2015 drought likely impacted juvenile SRFC in several ways resulting in decreased recruitment to ocean fisheries and subsequent adult escapement…. Low flows and elevated water temperatures associated with exceptional drought conditions in the Sacramento River Basin were experienced by outmigrating juvenile SRFC beginning in spring 2013 and these conditions persisted through spring outmigration periods in 2014 and 2015.

Note the plan report relates many of these early life history survival factors that have been identified over the past several decades. There is much documentation of these decades of data and studies in the plan report. Factors such as high water temperatures and redd dewatering have significantly reduced wild smolt production, especially during critical drought years.

2. Lower Hatchery Releases – “Hatchery releases were below average levels for the critical brood years, and offsite release practices utilized during drought conditions led to increased straying and river harvest of returning adults.”

The normal 26.7 million releases were reduced 17% in brood years 2012-14. Note some of these reductions in smolt releases were planned,2 while others involved difficulties in hatcheries in the critical drought years of 2013-2015.

3. Poor Ocean Survival – “for the critical brood years of 2012-2014, outmigrating juvenile SRFC encountered a wide range of ocean conditions. Poorer conditions in 2014 and 2015 were encountered by brood years 2013 and 2014.”

The primary issue appears to have been that hatchery juveniles released in the Bay generated adult survival, returns and harvest that were orders of magnitude higher than those of hatchery juveniles released in rivers.

4. Density Dependent Stock Recruitment – “High brood year 2012-2014 spawners from good 2010-2012 conditions led to high density dependent mortality and reduced escapement in 2015-2017” (Figure 2).

This statement appears to imply that excessive redd superimposition by overly abundant spawners in limited spawning habitat led to reduced wild smolt production. It is far more likely that poor returns from brood years 2012-2014 stemmed from other factors.

5. Trucking and Straying of Adult Hatchery Fish – “During the three years that contributed to the overfished status, no adults from onsite-releases were estimated to have strayed into the San Joaquin Basin. It was markedly different for offsite releases, however, and adults returning from offsite NFH releases actually strayed into the San Joaquin Basin at higher rates than those returning from offsite CNFH [Coleman National Fish Hatchery] releases. Stray rates generally increased each year during 2015-2017, and they were particularly high in 2017.”

There were many factors affecting hatchery returns from releases in critically dry years. One example is a pair of CNFH releases in April 2014, one at the hatchery in the upper river and one in the Bay (Figures 3 and 4). Although there was more straying from the Bay release group, there was also much greater survival (and fishery contribution). The fish released in the Bay did not have to pass through the lower 100 miles of the river in a drought year.

The river group was released under much higher flows (Figure 5) than the Bay group, which likely helped in return homing of the river release group. The Bay group was also larger (by 50% weight), having reared 20 days longer in the hatchery. It was wise to release all the 2015 CNFH smolts in the Bay to ensure survival and contribution to the fisheries, but they imprinted on a wide combination of Central Valley tributary flows leading to straying.

Another factor that likely increased CNFH returning adults straying was poor summer migrating conditions in the lower Sacramento River above the mouth of the Feather River (Figure 6). These conditions cause many returning adults to choose the American, Feather/Yuba, and Mokelumne Rivers.

6. Increased Harvest of Adult Stock – “Offsite-released fish were noticeably more prone to harvest once inside the Sacramento Basin. The entire SRFC stock experienced elevated in-river harvest rates during 2016 and 2017, largely due to the migratory behavior of spawners returning from offsite hatchery releases.”

Note higher harvest was also attributed to much better returns of Bay releases, as well as release timing and homing imprinting problems with Bay releases.

7. Hatcheries – “A common result across the CDFW reports is that hatchery-origin fish routinely make up the majority of natural area escapement and harvest, and at various levels of escapement.”

While hatcheries have these inherent problems, there would be few salmon and minimal salmon fisheries in California without hatcheries. However, the plan promotes the building of natural/wild components of SRFC populations. The problem is that adjusting and managing runs through fishery harvest management is not going to help make that happen.

The report recommends the following actions to rebuild the stock (fishable population) to allow Maximum Sustainable Yield (122,000 returning wild adults).

Recommendation 1 – rebuild in 3 years. Note the stock has met its goal since 2017 because brood-years’ 2015-2018 were reared in normal or wet years.

Recommendation 2 – adopt one of the alternative strategies:

  • Alternative 1 – status quo (rebuilds in three years
  • Alternative 2 – reduce harvest by 30 %
  • Alternative 3 – reduce harvest by closing southern-range ocean and all in-river fisheries (rebuilds in two years)

Recommendation 3 – eliminate or limit fall ocean fisheries

Recommendation 4 – limit harvest quota fisheries

Recommendation 5 – provide recommendations to the Council for restoration and enhancement measures within a suitable time frame. “It is recommended that the Council direct the Habitat Committee to work with tribal, federal, state, and local habitat experts to review the status of the essential fish habitat affecting SRFC and, as appropriate, provide recommendations to the Council for restoration and enhancement measures within a suitable time frame, as described in the FMP.”

Note that such processes have occurred on multiple occasions over the past several decades. Multi-stakeholder efforts abound, including the comprehensive the Central Valley Salmon and Steelhead Recovery Plan and various federal biological opinions and state take permits, as well as associated environmental reviews.

Further Recommendations

  • Consideration should be given to estimating productivity of natural-area spawners and
    development of management objectives for this component of the SRFC stock, as has
    previously been recommended by CA HSRG (2012) and Lindley et al. (2009).
  • How far did water quality deviate from optimal conditions.
  • Evaluate the effects of redd dewatering
  • Determine factors relating to straying of trucked hatchery smolts
  • Evaluate water temperature conditions in spawning reaches.
  • Evaluate why recovery has favored hatchery components

The plan also offers a summary:

Limitations on our ability to accurately explain and forecast annual variations in Pacific salmon production remain, in part because of uncertainty in the factors responsible for salmon mortality and from the effects of climate warming on the marine distribution and abundance of salmon. It is more important than ever to promote cooperative and innovative international research to identify and better understand the ecological mechanisms regulating the distribution and abundance of salmon populations for sustainable salmon and steelhead management. North Pacific Anadromous Fish Commission Bulletin No. 6: 501–534, 2016 .

Conclusion

Most of these recommendations miss the mark. The claim that there is too little understanding also misses the mark.

Sacramento River fall-run Chinook salmon escapement has benefitted from wet year periods (1995-2006 and 2010-2012; Figure 7) and off-site hatchery smolt releases to the Bay and ocean coast sites. Escapement has suffered immensely from drought conditions, which dramatically limited wild and hatchery juvenile survival (1987-1992, 2007-2009, and 2013-2015).

The plan should have focused more on the management of wild and hatchery smolt survival factors in drought years rather than adjustments to fishery harvest and hatchery production. As written, the plan will not improve the ability of the stock (population) to sustain harvest in the future, especially since the underlying problems are getting worse.

Figure 1. Sacramento River Fall Run Chinook total hatchery and in-river spawning escapement 1970-2017. SMSY = Maximum Sustained Yield target. MSST = Minimum Stock Size Threshold (minimum acceptable target). Note MSY target was not met in 2007-2009 and 2015-2017. Source of Figure: Salmon Rebuilding Plan.

Figure 2. Spawner numbers versus juvenile production index. Source of Figure: Salmon Rebuilding Plan.

Figure 3. Returns from April 4, 2014 SRFC smolts released at Coleman hatchery. Source: https://www.rmpc.org

Figure 4. Returns from April 24, 2014 SRFC smolts released in Bay. Source: https://www.rmpc.org

Figure 5. Daily Sacramento River flow at Freeport in April, 2014.

Figure 6. Migratory conditions for returning CNFH salmon in late summer. Blue regions are primary spawning areas. Green are migration and holding areas with adequate late summer water temperatures. Yellow areas are migration routes with excessive stressful water temperatures. Red area has blocking/lethal water temperatures. Note that conditions would encourage straying of upper Sacramento-bound salmon into cooler tributaries.

Figure 7. SRFC escapement 1975-2019.

  1. Pacific Fishery Management Council. 2019. Salmon Rebuilding Plan for Sacramento River Fall Chinook. Pacific Fishery Management Council, 7700 NE Ambassador Place, Suite 101, Portland, Oregon 97220-1384. https://www.pcouncil.org/documents/2019/07/sacramento-river-fall-chinook-salmon-rebuilding-plan-regulatory-identifier-number-0648-bi04-july-2019.pdf/ ↩
  2. https://calsport.org/fisheriesblog/?p=3262 ↩

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