Poor 2018 Sacramento River Fall Salmon Run Prognosis for 2019 Run

In an October 2018 post, I discussed the record low Sacramento River1 2017 adult fall-run Chinook salmon run and juvenile fall-run production index from winter-spring 2018. Both record lows were indications that something had gone wrong for brood year 2014. I also forecasted a poor adult run in fall 2018. The latest information on salmon runs for 2018, recently published by the California Department of Fish and Wildlife, indicates the 2018 fall run was indeed also poor (Figure 1). The run size in 2018 was 8980 (5th lowest in the record), as compared to 1822 in 2017, and 29,966 in 2014.

Despite a normal water year in winter-spring 2016 in the Sacramento River, the hangover from the critical 2013-2015 water-years drought (low reservoir levels) provided harsh conditions for brood year 2015 fall run that led to the poor adult run in 2018:

  1. Poor river conditions due to low streamflows during the spawning run in summer and late fall 2015 (Figure 2 and 3).
  2. Poor egg-embryo incubation in gravel redds due to low streamflow in late fall 2015 and early winter 2016 (Figure 2).
  3. Poor fry survival from low winter streamflows (February and early March) and poor smolt survival from low late spring streamflows (late April and May) in 2016 (Figure 3).

In addition, most of the 10 million Coleman Hatchery smolts raised for brood year 2015 were released at the hatchery in lower Battle Creek from April 7 to April 29, 2016, under sharply declining streamflows (Figure 3) and rising water temperatures in the lower Sacramento River (Figure 4). Their contribution to the 2018 spawning cohort was similarly low. Of the 10 million smolts released, only 14,000 adults returned to the upper river, as compared with 84,000 in 2012.

Based on the spawner recruit model, the 2018 fall run of 8980 adult salmon could have been three times as high or higher (similar at least to 2012 or 2014) if not for poor river flows and associated high spring water temperatures that exceeded water quality standards.

The prognosis for the upcoming 2019 run is mixed, but the run should show improvement. Early indications are good,2 despite very low numbers of spawners in fall 2016 (red 16 in Figure 1). Water year 2017 was wet (19 will be blue in Figure 1). Coleman Hatchery’s released 10-million smolt to the upper river in April 2017 under optimal conditions. There were stressful warm water (>20oC) and low flow conditions in July-August 2016 early in the 2016 spawning run (Figure 5), as well as low and sharply dropping flows in the fall spawning season that likely caused some redd dewatering and low egg/embryo survival. Maintaining less than stressful water temperature during the early run in summer will be important; conditions are already marginal during late spring when winter-run and spring-run adults are migrating (Figure 6). Flows in the 10,000-14,000 cfs range may be necessary to maintain water temperatures at or below 20oC through the summer. With Shasta Reservoir full and an abundant snowpack, that should be readily achievable.

Hopefully, the 2019 run can approach that of 2012 (green 12 in Figure 1) for that low level of spawners (09 and 16 were similar). The results for summer coastal and river fisheries will be the next indicator of success for the 2019 fall-run salmon.

Figure 1. Spawner-recruit relationship for Sacramento River fall-run in-river estimates of run size (transformed log10-3). The 2018 escapement is shown as large blue dot and associated green “18”. Number indicates spawner estimate for that year (y-axis) as derived from spawners three years earlier (x-axis). Color indicates winter-spring rearing and migration conditions for that brood (winter-spring 2016 for spawners in 2018). Red denotes dry year in first winter-spring. Green denotes normal years. Blue denotes wet years. The 2018 spawner (escapement) number should have been higher, similar to other normal water years. Source: http://calsport.org/fisheriesblog/?p=2333 .

Figure 2. Streamflow in the upper Sacramento River below Shasta/Keswick dams near Redding July 1, 2015 to June 30, 2016. Source: USGS. Note the low late fall and winter streamflows in the primary spawning grounds below Keswick Dam. The decline from 7000 cfs in late October to below 4000 cfs in late December led to significant redd dewatering and poor fry survival. Fall-winter flows should not fall below 5000 cfs.

Figure 3. Streamflow in the lower Sacramento River near Grimes, July 1, 2015 to June 30, 2016. Source: USGS. Note the low summer and fall streamflows in 2015, and low late spring flows in 2016. Poor pre-spawn and spawning season (summer-fall) flows lead to poor adult survival to spawning and poor egg viability. Low spring flows lead to high water temperatures and lower turbidities that increase smolt vulnerability to predation. Flows in the lower river should be maintained above 5000 cfs.

Figure 4. Water temperature in lower Sacramento River at Wilkins Slough in April-May, 2016. Note the Basin Plan water quality standard for lower Sacramento River water temperature requires temperatures no greater than 20oC, 68oF. High water temperatures lead to poor migrating smolt growth and greater vulnerability to predation. Spring water temperatures should not exceed 18oC, 65oF to minimize migrating smolt mortality.

Figure 5. Water temperature and river flow in the lower Sacramento River near Grimes from July 2016 to June 2017. Note that water temperature exceeds 20oC , the stress level for adult salmon and water quality standard, when summer flows fall below about 8000 cfs.

Figure 6. Water temperature and river flow in the lower Sacramento River near Grimes in May 2019. Note that in mid- and late May, water temperature reached near 20oC, the stress level for adult salmon and water quality standard, when flows initially fell to near 8000 cfs.

Brood Years 2011-2013 Feather Hatchery Survival to Adulthood What was learned?

The number of fall-run salmon released from the Feather River Fish Hatchery that are either captured in fisheries or that return to the Feather River as adults (% survival) varies from year to year and within each year.1 Recent patterns of survival to adulthood from brood years 2011-2013 provide insights into the effectiveness and potential success of different strategies for releasing smolts from the hatchery.

Brood Year 2011

DFW released nearly 7 million 2011 brood year smolts in spring 2012. Survival improved as fish were released with later in the season, with highest survival for late-released older smolts on the coast at Half Moon Bay (Figure 1). The declining late spring survival for the San Pablo Bay releases may be related to low late spring Delta Outflow in this below-normal water year (Figure 2). The late-season Half Moon Bay release group had a 5% rate of survival (Table 1), as compared to about 2% for late season releases from San Pablo Bay (North-East San Francisco Bay). Approximately three-quarters of survival to adulthood was accounted for in reports of fish captured, with the remainder from counts at spawning grounds and hatcheries.

Brood Year 2012

From the approximately 6.5 million Feather hatchery smolts of brood year 2012 released in spring of drought year 2013, Golden Gate releases had the highest survival rates at near 4% (Figure 3). Lower Sacramento River releases had poor success, with a survival rate to adulthood of less than 0.1%. This poor outcome is likely a consequence of low flow and high water temperatures in the river (Figures 4 and 5). Bay releases had relatively good returns of approximately 1.4-2.3% under relatively good Delta outflow conditions.

Brood Year 2013

Among the approximately 6.5 million Feather hatchery smolts of brood year 2013 released in spring of critical drought year 2014, most groups survived poorly (<1%; Figure 7). The group released to Half Moon Bay on the coast was an exception at 3.3%. One group released in San Pablo Bay on April 29 had a modest survival rate of 1.3%; their release occurred during a period of slightly higher Delta outflow (8000-9000 cfs; Figure 8). Other groups released to Bay or Delta had low survival; their release occurred under very low Delta outflow (3000-5000 cfs).

Straying

The most commonly stated concern for trucking and barging smolts to the Delta, Bay, Golden Gate, and coastal bays is straying of adult spawners to other rivers and hatcheries.

  1. The highest performing groups, HMBay releases, had the highest risk of straying being trucked to the coast outside the Golden Gate. Of the BY 2011 group’s (Table 1, Figure 1) hatchery returns, 534 (90%) were to its origin hatchery on the Feather River. This compares with the 91% return for corresponding release to San Pablo Bay net pens. This compares to 96% for the FR group.
  2. Golden Gate releases had similar straying rates. For BY 2012 (Figure 3), trucked smolts had 92% of hatchery returns to the origin hatchery, while barged fish had 93% return. These rates compare to 81% of hatchery returns to origin hatchery for the 5/23 SPB net pen group. Only two fish returned to Central Valley hatcheries (both to Feather River Hatchery) from the BY 2012 FRiv group.

Summary

  • The rate of survival to adulthood of hatchery release groups was higher in wetter years.
  • Early spring (prior to mid April) smolt releases had lower survival rates than later spring releases.
  • Survival of smolts released in-river was modest in wetter years and very poor in dry years.
  • Highest rates of survival (4-5%) were from Half Moon Bay on the coast south of San Francisco.
  • San Pablo Bay pen release return rates were better (2-3%) under higher Delta outflow; returns were poorer (<1%) when San Pablo releases occurred during periods of low Delta outflow (3000-5000 cfs).
  • Straying rates overall were generally low (5-10%). The lowest straying rate (4%) was from river release at mouth of Feather River.

Conclusions

Coastal and Golden Gate smolt releases provide the highest rates of survival to adulthood. Stray rates for these release groups are low. Rates of survival for smolts released in-river and in San Pablo Bay are poor in drier years with low Delta outflow.

The best strategy for high rates of survival would appear to be to make most or all releases in drier years at the coast and the Golden Gate, and to make releases in wetter years in-river and in San Pablo Bay. Releases of smolts to the rivers in dry years and in years with poor Delta outflow should be avoided, especially during late spring when flows are low and water temperatures are high.
Table 1. Returns from Tag Group 060374 released at Half Moon Bay.

Figure 1. Survival rates for brood year 2011 Feather River Hatchery smolts released in spring 2012. GG is Golden Gate. SPB is San Pablo Bay. FR is Feather River. HMBay is Half Moon Bay along the coast south of San Francisco.

Figure 1. Survival rates for brood year 2011 Feather River Hatchery smolts released in spring 2012. GG is Golden Gate. SPB is San Pablo Bay. FR is Feather River. HMBay is Half Moon Bay along the coast south of San Francisco.

Figure 2. Delta outflow in spring 2012.

Figure 2. Delta outflow in spring 2012.

Figure 3. Survival rates for brood year 2012 Feather River Hatchery smolts released in spring 2013. GG is Golden Gate. SPBNP is San Pablo Bay net pen. FRiv is Sacramento River below mouth of Feather River. HMBay is Half Moon Bay. SCruz is Santa Cruz harbor.

Figure 3. Survival rates for brood year 2012 Feather River Hatchery smolts released in spring 2013. GG is Golden Gate. SPBNP is San Pablo Bay net pen. FRiv is Sacramento River below mouth of Feather River. HMBay is Half Moon Bay. SCruz is Santa Cruz harbor.

Figure 4. Sacramento River flow below mouth of the Feather River in spring 2013, along with historical average. Note lower than average flow in April and early May.

Figure 4. Sacramento River flow below mouth of the Feather River in spring 2013, along with historical average. Note lower than average flow in April and early May.

 Figure 5. Sacramento River water temperatures below mouth of the Feather River in spring 2013, along with historical average. Note that water temperatures in spring 2013 were about 5oC above the long-term average through early June.

Figure 5. Sacramento River water temperatures below mouth of the Feather River in spring 2013, along with historical average. Note that water temperatures in spring 2013 were about 5oC above the long-term average through early June.

 Figure 6. Delta outflow in spring 2013.

Figure 6. Delta outflow in spring 2013.

Figure 7. Survival rates for brood year 2013 Feather River Hatchery smolts released in spring 2014. GG is Golden Gate. SPBNP is San Pablo Bay net pen. Rio Vista is North Delta. HMBay is Half Moon Bay.

Figure 7. Survival rates for brood year 2013 Feather River Hatchery smolts released in spring 2014. GG is Golden Gate. SPBNP is San Pablo Bay net pen. Rio Vista is North Delta. HMBay is Half Moon Bay.

 Figure 8. Delta outflow in spring 2014.

Figure 8. Delta outflow in spring 2014.

Survival to Adulthood of American River Hatchery Salmon

The Nimbus Fish Hatchery on the American River produces approximately 4 million fall-run Chinook salmon smolts each year for release to the American River and to San Pablo Bay (after being held there in net pens). Releases are made from late April to early June. Release return rates are available for 2007-2015.1 In 2014 and 2015, all releases were to the Bay. From 2016 to 2018, a substantial proportion of releases were to the American River.

Return rates (percent captured as adults in fisheries plus percent returning as adults to spawning grounds and the hatchery) from 2007 to 2015 releases varied from 0.3 to 3.7 percent (Figure 1). Return rates were higher for wet year 2011 and normal years 2010 and 2012. Return rates for river and Bay release groups were similar in wetter years. Overall return rates in dry years were lower than return rates in wetter years, with higher returns for Bay release groups than for river release groups.

River return rates were low in years with lower flow and higher water temperature in the lower American River. American River flow was lower in late spring 2009 and 2013 (Figure 2). River temperatures were higher (>55oF) in these drier years (Figure 3), as were Delta temperatures (>68oF; Figure 4). Such conditions are detrimental to smolt survival.

Poor returns (<1%) from dry year Bay releases (<1000 cfs Delta outflow) are associated with low Delta outflows (<10,000 cfs, Figure 5). Lower ocean survival may have also contributed to poorer Bay release returns.

Conclusions and Recommendations

An optimal strategy for increasing the contribution of Nimbus Hatchery’s 4 million fall-run Chinook salmon smolts would be:

  1. Release smolts in the American River in wetter years with higher river flow and lower river water temperature.
  2. Release smolts in the Bay in dry years; do not release in river.
  3. Maintain Delta outflows above 10,000 cfs during periods of release of smolts to the Bay.

This strategy could increase hatchery smolt returns as much as 1%, or by 40,000 adult salmon, assuming 4 million smolts. In drier years, this would double or triple the contribution from the American River hatchery to salmon available for catch and to salmon returning to the American River to spawn.

Figure 1. Return rates for Nimbus Hatchery smolt late spring releases to the American River (red dots) and San Pablo Bay (black color dots).

Figure 2. Lower American River flows 2009-2013. Red dots indicate periods of release of hatchery smolts to the river.

Figure 3. Water temperatures in the lower American River from 2009 to 2015. Red dots indicate periods of release of hatchery smolts to the river.

Figure 4. Water temperatures in the north Delta 2009 to 2015. Red dots indicate periods of release of hatchery smolts to the river.

Figure 5. Delta outflows 2007-2015. Red circles indicate periods of release of hatchery smolts to the Bay.

Response to Bay-Delta Science Paper on The Problems with Coleman Hatchery Salmon Straying

In a Maven 1/17/19 post, US Fish and Wildlife Service hatchery managers discuss problems that have developed from trucking salmon smolts from the Coleman National Fish Hatchery (Coleman NFH) to San Francisco Bay. Chief among these problems is that juvenile fish trucked from Coleman NFH stray into other Central Valley rivers as spawning adults, rather than returning to Coleman NFH. This has become a general argument for releasing Coleman NFH smolts near Redding instead of trucking or barging them to the Bay.

During the 2013-2015 drought, many Coleman NFH smolts were trucked to the Bay for release to meet the hatchery’s goals:

The management goals for the hatchery are to provide about 1% of their production or about 120,000 fish from each brood year to the ocean fishery, the freshwater sport fishery, and returns to Battle Creek for brood stock, all while trying to reduce negative impacts on naturally spawning fish.

From 2013-2015, 35.5 million fall run smolts, about 12 million per year, were reared for release by the Coleman NFH. In 2013, all were released at the hatchery into Battle Creek. In 2014, 3.4 million were released at the hatchery, and the remainder were trucked to the Bay. In 2015, all 12 million were trucked to the Bay. Since 2015, all Coleman NFH fall-run smolts have been released at the hatchery.

Trucking during the drought did meet the 1% production goal, but did not provide adequate hatchery returns for broodstock and did not achieve low straying rates.1 The USFWS has since chosen to ignore the production goal in order to achieve the other two goals. In dry years, the 12 million smolts now provide 10,000-20,000 adults (0.1-0.2%) to fisheries instead of 100,000-200,000 (1-2%). Instead of increasing hatchery production by barging smolts or improving post-release river conditions (higher flows), the fall-run salmon production program at Coleman NFH, designed explicitly as mitigation for loss of salmon from the federal Central Valley Project, is not meeting its primary mitigation goal.

In the response to Maven’s questions on USFWS presentation at the Bay-Delta Science Conference, the USFWS managers offered the following responses:

Is Straying Bad?

  • This occurs because fish that do not naturally emigrate through the river system lose the opportunity to imprint properly and may be unable to locate their natal area when they are ready to spawn. Response: High stray rates are unique to the federal Battle Creek Coleman NFH, partially because many of their returning adults spawn in the upper Sacramento River (as intended) and do not move into Battle Creek, and are thus considered strays. Regardless of imprinting influence, returning adults to the Sacramento River are confronted with poor flows and high water temperatures above the mouth of the Feather-Yuba-Butte Creek, Mokelumne, and American rivers, so they choose those rivers out of necessity. This problem does not occur at the Feather, American, and Mokelumne state hatcheries. These other hatcheries have also transported stray, earlier-returning Battle Creek adults (or fertilized eggs) to the Coleman Hatchery to help Coleman offset its egg shortages.
  • Hatchery fish that stray into natural spawning areas can detrimentally affect natural fish populations through genetic, ecological, and behavioral mechanisms…. Increased straying by hatchery fish may reduce genetic diversity within and among salmon populations. Response: While this is generally true for pristine natural salmon watersheds, this concern was long ago lost in the Central Valley after a century of disturbance and hatchery interference. Eggs have been shared, even from out of state, and even from different runs (hatcheries and dams have forced mixing of spring-run and fall-run spawners). Hatchery strays continue to dominate runs in non-hatchery rivers; without the strays, there would be few if any salmon in these rivers. Straying is also a natural process needed to retain population fitness, resilience, and genetic diversity.
  • Likely due to the prevalence of off-site release practices at Central Valley hatcheries, Central Valley fall Chinook Salmon have lost locally adapted genes and become one large, genetically homogeneous population (see Johnson et al 2012). Response: Adapted genes were lost decades ago before off-site releases. Johnson et al were describing how hatchery dominance covers up underlying problems in wild populations, not necessarily how it causes the underlying problems. This is a real concern in the Central Valley where only 25% of the fall run hatchery smolts are marked. The true wild components of individual river runs need protection. For some rivers, natural spawning areas can be reserved for true wild spawners (e.g., Battle Creek, Yuba River, Mokelumne, Calaveras, Butte Creek, etc.). Wild spawners can also be relocated above rim dams. Conservation hatcheries can use “wild” spawners.
  • Furthermore, salmon that are spawned and reared in fish hatcheries may become quickly adapted for characteristics that favor their survival and reproductive success in the hatchery environment while, at the same time, diminishing their ability to survive and reproduce in the natural environment. Response: while potentially (and historically) true, modern hatchery programs minimize or should minimize, if not reverse, these tendencies.
  • Stray hatchery fish may also compete with natural fish populations for limited resources, including competition for preferred spawning areas by adults and competition for food resources and habitat by juvenile fish. Response: Again, while generally and historically true, hatchery adult returns now take the place of wild adults in increasingly depressed amounts of spawning habitat in Central Valley rivers. Also, it is generally known that in many cases wild adults out-compete hatchery adults for habitat. Also, in most Central Valley rivers, hatchery fall-run adults can be effectively excluded from primary spawning areas. Hatchery smolts can readily be excluded from natural rearing areas by controlling timing and location of releases. In arguing against barging or trucking, USFWS managers are in essence arguing to continue releasing their hatchery smolts into prime natural rearing areas.
  • When hatchery fall Chinook Salmon from Coleman NFH stray at high rates, the freshwater fishery may be redistributed to other parts of the Central Valley and sport fishing in the upper Sacramento River fishery is negatively impacted. Response: Low flows and high water temperatures are the biggest contributor to poor upper Sacramento River salmon fishing.2 Also, Coleman hatchery adults that spawn in the upper Sacramento River or that are caught by sport fisherman in the Sacramento River upstream of Battle Creek are considered strays, even though they are produced to mitigate for Shasta Dam.
  • High stray rates of trucked hatchery fish may impact the ability of Coleman NFH to meet its annual fish production targets. For example, in 2017 (which corresponded to age-3 adult returns of fish that were 100% trucked), less than 350 adult salmon returned to the hatchery. At a minimum, Coleman NFH needs to spawn 2,600 pairs of adult salmon to meet the production target of 12 million juveniles. As a result, Coleman NFH released less than 6 million juveniles in the spring of 2018, which will result in fewer fish available to achieve our management goals in future years. Response: Then why not release a portion of the smolts in the Bay as for brood year 2013 (2014 releases)? Other potential measures to increase egg take outlined by the authors can also be enhanced.

Need for Trucking

  • California’s drought had some negative impacts for Coleman National Fish Hatchery….The one percent contribution goal to the fisheries and returns to Battle Creek was not able to be achieved under the drought conditions. Response: The drought was not to blame. Reclamation’s water right permits require measures to protect salmon, even during droughts. During the 2013-2015 drought, Reclamation delivered too much water to Sacramento River settlement contractors. This left Reclamation too little water to meet the conditions in its water rights permits that are designed to protect salmon. Water management during droughts is the problem.
  • Despite our extra efforts to collect additional eggs, we only met about half of our production target. We’ve undertaken a study to assess fish survival under different release strategies. This information will hopefully allow for adaptive management, based on changing environmental conditions and may give us some flexibility to release fish onsite to meet our multiple management goals in the future. Response: If Reclamation provides environmental flows from Shasta, and if USFWS times releases of hatchery juveniles at Coleman NFH to water conditions, then Battle Creek releases may produce more adult salmon. Some amount of trucking may be necessary to meet overall mitigation goals.

Conclusion

Hatchery program managers should not give up on trucking and on reducing high stray rates. They should consider barging juvenile salmon to better imprint smolts and improve smolt survival. Federal water managers also need to improve lower Sacramento River conditions for returning adults, in order to reduce straying. Water contractors and state/federal purveyors must also collectively limit their water diversions to meet water right permit conditions and water quality standards that are designed to protect fish. Egg taking should be increased if hatchery releases are to continue, in order to meet mitigation goals. These measures will all help hatchery managers meet their adult production goals and mitigation commitments. Trucking, a standard practice at state hatcheries in all year types, may be necessary, especially in periods of drought, to meet mitigation goals.

Washington State increasing hatchery salmon production Major realignment toward wild population recovery

Washington State is increasing salmon production to help in recovery of near extinct salmon populations and orca (killer whales). A Washington state Department of Fish and Wildlife webpage describes the role of hatcheries in restoring wild salmon stocks:

In recent years, state hatcheries also have taken on an equally important role in helping to recover and conserve the state’s naturally-spawning salmon populations. Nearly all the hatcheries in the Columbia River and a number of hatcheries in Puget Sound play a role in wild fish rebuilding programs, whether by rearing juveniles prior to release or holding fish through their lifespan to ensure the survival of depressed stocks. This renewed focus on wild stock recovery represents a major realignment in hatchery operations, as WDFW, the tribes, federal government and independent scientists worked to develop a comprehensive operations strategy for hatcheries in Washington. 1

The main reform actions being taken in Washington’s program are:

  1. Marking all hatchery salmon smolts allows identifying hatchery fish by hatchery and lot group. It also allows mark-selective fisheries that require release of wild salmon.
  2. Developing salmon population-specific recommendations intended to provide scientific guidance for managing each hatchery more effectively in the future.
  3. Keeping hatchery program budgets in pace with increasing operating costs (especially utilities, fish feed and labor costs), and not forcing cutbacks in some programs.
  4. Updating aging hatchery infrastructure.
  5. Supplementing wild stocks: to maximize egg fertilization and fry survival (of wild) and thereby increase the number of “wild-type” smolts heading out to the ocean.
  6. Maintaining captive broodstocks of endangered stocks with dangerously low population levels: juveniles are maintained in a hatchery for their entire life to ensure the stock’s survival.
  7. Minimizing interaction between naturally-produced and hatchery-produced outmigrating juveniles and adult fish returning to streams to spawn where necessary.
  8. Donating surplus adult salmon from hatcheries to non-profit hunger-relief programs.
  9. Introducing hatchery carcasses or analogs back to streams to increase natural productivity to low productivity streams.

While California is slowly moving toward some of these reforms, there is resistance to others. For more information and links on California hatchery programs see http://calsport.org/fisheriesblog/?cat=5 , https://www.wildlife.ca.gov/fishing/hatcheries , http://cahatcheryreview.com , https://www.fws.gov/sfbaydelta/Fisheries/hatcheries/NoCAHatcheriesUSFWS.htm .