Category Archives: Hatcheries

Wishful Thinking on The Upcoming 2022 Salmon Season

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We should be careful about wishful thinking in considering the forecasts for the 2022 California salmon season along the coast and in major rivers.1  The 2022 ocean abundance projection for Sacramento River fall Chinook, a main salmon stock harvested in California waters, is estimated at 396,500 adult salmon, a higher number than the 2021 forecasts. However, we should expect further drought-related fishery and escapement downturns in 2022 and 2023, as occurred after the 2007-2009 and 2013-2015 droughts (Figure 1). We can also expect low fishery catches, especially in rivers from low summer flows and associated high water temperatures that keep river spawners in the Bay until rivers cool in the fall.

The issues relate primarily to remaining stocks of Chinook salmon, not to the nearly extinct endangered Coho. The 2022 season also relates mostly to the availability of brood year 2019 salmon from Central Valley rivers, not coastal streams. Finally, it is important to remember that most of the adult salmon in 2022 will come from hatcheries on the Klamath, Trinity, Sacramento, Feather, American, Mokelumne, and Merced rivers, especially those hatcheries that truck and barge salmon to the Bay or coast.

Hatchery returns, the backbone of California salmon fisheries, are likely to be lower in 2022 than expected. Near 40 million Chinook salmon smolts from brood year 2019 were released from California federal and state hatcheries in 2020. Of the total, about 26 million were raised at Sacramento River watershed hatcheries, 9 million at San Joaquin River hatcheries, and 4 million at Klamath-Trinity hatcheries. Most of the releases were fall-run (34 million), with about 4 million spring-run, 1 million late-fall-run, and 0.4 million winter-run. Their returns of jacks and adults are likely to be lower in 2022 than expected because of low Delta inflows and outflows (Figure 2) and low Klamath-Trinity flows (Figures 3 and 4) in winter-spring 2020 and 2021, which are likely to result overall in relatively poor returns from river and Bay releases of hatchery smolts.2

Wild salmon stocks, already severely depressed, are going to further decline and contribute even less to fisheries. Natural production of brood years 2019 and 2020 was likely poor because wild smolts faced dry-year conditions in winter-spring 2020 and 2021, respectively.

Adult salmon that return to spawn in 2022 will face warm rivers, as they did in 2021 (Figures 5 and 6). They will be delayed, and many will die before spawning.

In summary, we must be careful about wishful thinking about the future based on the recently released ocean abundance estimate for 2022. Many other factors point in a downward direction. Perhaps the most immediate question is whether “salmon will simmer again” in what looks to be a dry, hot summer.

Figure 1. Sacramento River Basin fall-run salmon escapement 1975-2020.

Figure 2. Sacramento-San Joaquin Delta outflow 2014-2022.

Figure 3. Klamath River flow at Orleans 2014-2022.

Figure 4. Trinity River flow at Hoopa 2014-2022.

Figure 5. Flow and water temperature in the lower Sacramento River at Wilkins Slough in 2021. Red line is 20ºC (68F) water quality standard and safe upper level for salmon.

Figure 6. Water temperature at Wilkins Slough in 2021 and recent historical average.

Salmon Released from Central Valley Hatcheries

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Hundreds of thousands of smolts of endangered salmon are being released to the lower Sacramento River from federal and state hatcheries this winter, the San Francisco Chronicle reported on March 2.1 It is a drought year, and most of the young salmon will likely perish in the jaws of predators on their 300-mile journey to the ocean through the river, Delta, and Bay. Without the protection of adequate river flow, cold water, and turbidity for the journey, there is little hope. Reservoir storage is depleted from the past two years of overzealous water deliveries. What little rain and snowmelt there has been in the Valley is being stored in reservoirs. Warm weather has come early. The 400 thousand smolts released on March 2 could use some help, but they have not received it and are not likely to get it.

River Flow

Flow from Shasta Reservoir to the upper river via Keswick Dam has been minimal (Figure 1, KWK). 40 miles downstream at the Bend (BND) gage near Red Bluff, the river received some snowmelt from tributaries in January, but even that tapered off by the end of January. Flow into the Delta from the Sacramento Valley at Freeport (FPT) reached minimal levels by the end of January. Delta outflow (Figure 2) settled at its minimal prescribed level near 12,000 cfs after some January export taking.

Water Temperature

Warm weather and low flows have allowed water temperatures in the lower Sacramento River and north Delta migration corridor to reach the mid-fifties (Figure 3), temperatures that activate lower river predators like striped bass, resident trout, and pikeminnow.

Turbidity

Turbidities (Figure 4) are now at seasonal lows from the upper river near Red Bluff (RDB) to the Delta near the Rio Vista Bridge (RVB), reflecting clear waters needed by sight-feeding predators like striped bass.

Delta Salmon Salvage

Hatchery salmon smolts released in December at least reached the Delta during the December storms (Figure 5). It remains to be seen if the February and March smolt releases even reach the Delta.

What’s Needed

The article in the Chronicle mentioned that only one of the 140 radio-tagged hatchery smolts released in February has reached the Delta. The March 2 release of 400,000 smolts could use a pulse of cold turbid water from Shasta, Oroville and Folsom reservoirs to help them reach the Bay. So far, only Oroville releases have increased, from 3500 to 5500 cfs in recent days, with the added 2000 cfs showing at Freeport (Figure 1). While this helps near the Delta, it does little for the upper 200 miles of river the smolts have yet to transit.

Figure 1. River flows near Keswick (River Mile-RM 300), Bend (RM 250), and Freeport (RM 50) in winter 2022.

Figure 2. Delta outflow in tidally averaged daily cfs in winter 2022.

Figure 3. Water temperature in Sacramento River near Bend (RM 250), Wilkins Slough (RM 140) and Freeport (RM 50) in winter 2022.

Figure 4. Water turbidity in Sacramento River near Bend (RM 250), Red Bluff (RM 240), Freeport (RM 50), and Rio Vista (RM 30) in winter 2022.

Figure 5. Salmon salvage observed at Delta Fish Facilities in water year 2022.

American River Hatchery Salmon Releases – 2020/2021

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Escapement of American River fall-run salmon dropped after recent drought years (2013-2015, Figure 1).  It is reasonable to expect it would fall again in 2022 and 2023 as a consequence of the 2020-2021 drought period.

In a November 2, 2021 post, the California Department of Fish and Wildlife (CDFW) announced a plan to increase releases of hatchery smolts from its Nimbus Fish Hatchery on the American River in 2022, from the normal 4 million to 4.5 million.  CDFW’s post stated in part:

“Chinook salmon returns to the American River declined significantly during California’s last drought,” said Jason Julienne, supervisor for CDFW’s North Central Region fish hatcheries. “We’re using those observations and that experience to get ahead of any population declines this time around by increasing production to help sustain this important salmon run.”

In a June 2020 post, I summarized annual hatchery releases of American River fall-run salmon smolts for years 1991-2019.  I suggested that the long-term declines in escapement were also due to reductions in overall smolt releases and to an increasing proportion of river releases as opposed to Bay releases in drier years (Figure 2).

In 2020, a total of 4.44 million smolts were released, with 2.63 million released to the river and 1.81 million to the Bay (Figure 3).  The 1.6-million smolts released in-river in May 2020 were subject to low flows in the river and the Delta and to high water temperatures (Figures 4 and 5).  As a consequence, I would expect 2022 escapement to follow the general downward trend.

In drought year 2021, all 4 million smolts were trucked and released to the Bay.  However, I still expect 2023 escapement to be reduced as a consequence of the generally poor survival of smolts released to the Bay in drier years with low Delta outflow.1

Until flow conditions in the river and Bay in dry years improve, a 12.5% increase in hatchery smolt releases is unlikely to improve escapement to recent historical levels.

Figure 1. American River fall-run escapement to river and hatchery 1975-2020.

Figure 2. American River hatchery smolt releases to Bay and river 1991-2019.

Figure 3. American River hatchery smolt releases to Bay and river in 2020.

Figure 4. American River streamflow and water temperature in spring 2020.

Figure 5. Sacramento River water temperature below the mouth of the American River near Freeport in spring 2020.

Hatchery Delta Smelt 2021

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Efforts continue to gain approval for releasing hatchery-raised delta smelt in the San Francisco Bay-Delta Estuary. However, given a poor prognosis for a successful introduction, the chances of approval are not good.1  The biggest obstacle is the absence of a location to release the hatchery-raised fish that will allow their survival and thus contribute to the species’ recovery. Another problem is the potential detrimental effect on the remaining wild smelt from genetic compromise.

To me, the answer to the second issue is clear. With few if any “wild” delta smelt left on Earth, it is essential to get as many hatchery smelt out into the wild as soon as possible to save the species. Let the genetics get worked out later by Mother Nature.

Two locations for release of hatchery smelt seem most plausible: the low salinity zone in the west Delta/eastern Suisun Bay and the Deep-Water Shipping Channel in the north Delta. These are primary late spring and early summer nursery areas that are most likely to have the right habitat conditions (water temperature and low salinity) and food supply. These two locations were the last known concentrations of juvenile delta smelt (Figure 1) from the last strong adult spawn in 2012 (Figure 2).

The better of the two sites is the eastern-Bay/west-Delta location, because the ship-channel gets too warm by summer (Figure 3). In contrast, the region between Collinsville in eastern Suisun Bay and Decker Island in the west Delta is cooler and within the low salinity zone (Figures 4 and 5). A nighttime near-bottom release into cooler, deeper channel waters would give the hatchery smelt at least a minimum opportunity to acclimate to the warm Bay-Delta waters.2

Figure 1. Last known prime late spring and early summer nursery area of delta smelt (2012, 20-mm survey). Red lines denote approximate location of X2 (~2000-4000 EC) at the time.

Figure 2. Adult delta smelt catch index from monthly winter trawl surveys 2002-2021.

Figure 3. Water temperature (ºC) and salinity (EC) in spring 2020 in Deep Water Ship Channel.

Figure 4. Water temperature (C) and salinity (EC) in spring 2021 in Sacramento River channel near Collinsville in eastern Suisun Bay.

Figure 5. Water temperature (ºC) and salinity (EC) in spring 2021 in Sacramento River channel near Decker Island in the western Delta.

Lessons in American River Hatchery Management Based on Returns from 2016 and 2017 Salmon Smolt Releases

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The American River provides approximately 20-40% of the Central Valley fall Chinook run each year. Most of the American River run is derived from hatchery smolt releases from the Nimbus American River Hatchery. In this post, I suggest hatchery and water management actions to increase the ratio of adult returns per hatchery smolt releases to enhance fishery benefits from the American River hatchery.

This post builds on earlier posts. In a July 2020 post, I described how the American River was “shortchanged” on hatchery production, resulting in declining runs and less contributions to ocean and river fisheries. In a May 2019 post, I supported a hatchery strategy that included smolt releases to the river in wet years because river releases survived as well as smolts trucked to the Bay in wet year 2011. I also promoted trucking to the Bay in drier years, because of poor adult returns from river smolt releases in dry years.

Recent data indicate that trucking provides benefits even in wet years, with limited drawbacks. Water year 2017 was the first wet year since 2011. Returns from the 2017 releases indicate a distinct advantage of trucking smolts to the Bay over river releases (Figure 1). Trucking to the Bay enhanced returns of adult salmon by 250%, although river smolt releases had reasonably good survival (>1%). Returns from below-normal water year 2016 smolt releases (Figure 2) were poor for river releases as expected, but were also lower for Bay releases compared to 2017 releases.

Detailed results from the 2016 and 2017 release groups support trucking smolts to the Bay even in some wet years. Water years 2016 and 2017 provide a good contrast in hatchery smolt return patterns for dry and wet year smolt release strategies, focusing on the differences observed between river and Bay releases. In both years, all smolt releases occurred in late May and early June. Past strategies of late April or early May releases have proved less successful, despite the potential concerns of poor late spring river conditions. It appears that larger smolts have a greater chance of survival regardless of the release strategy.

2016 Smolt Releases

  • River smolt releases in 2016 were in mid-May. River conditions were good, with flows of 4,000-5,000 cfs and water temperatures below 60oF (Figure 3). These smolts then had to contend with marginal Delta and Bay conditions (Figures 4-6) on their journey to the ocean. Water temperatures in the Delta in the two weeks following the releases rose from 66 oF to 73 oF (stressful to near-lethal levels), as Delta outflow declined from 14,000 cfs to 7000 cfs.
  • Bay smolt releases in 2016 were in early June, with Delta outflow around 7000 cfs (Figure 4). Water temperatures were stressfully warm around the Bay release site at 66-70 oF (Figure 6).
    2017 Smolt Releases

2017 Smolt Releases

  • River smolt releases in 2017 were in late May. American River conditions were good, with flows of >6000 cfs and water temperatures below 60oF (Figure 3). These smolts also had high flows (>50,000 cfs) and near optimal Delta and Bay conditions on their journey to the ocean.
  • Bay smolt releases in 2017 were in early June under near optimal conditions, with Delta outflow around 20,000-30,000 cfs (Figure 4).

River vs Bay Releases

  • Returns from river smolt releases continued to be very poor in dry year 2016 (0.1-0.3%, Figure 2), while being measurably improved in a wet year 2017 (1.03-1.23%, Figure 1).
  • Returns from Bay smolt releases in dry year 2016 (0.9-1.67%, Figure 2) were lower than in wet year 2017 (2.64-2.71%, Figure 1).
  • Overall, Bay releases in dry year 2016 had return rates 3 to 10 times higher than river releases. In wet year 2017, Bay release returns were 2.5 times higher than returns of river releases.

Bay releases in a wet year and a dry year

  • Bay releases provide higher returns with higher Delta outflow (Figure 7), continuing the pattern previously noted. Survival in wet year 2017, when outflow exceeded 10,000 cfs-20,000 cfs, was nearly double that in dry years 2016. A combination of lower net transport flows and higher water temperatures (Figure 6) in 2016 likely explains why returns from Bay smolt releases in 2016 was 50% of returns from Bay smolt releases in 2017.

Straying of adult returns from Bay and river releases

Straying of adult returns originating from the American River hatchery to other rivers remains an issue with off-site hatchery smolt releases (trucking to the Bay). Though the proportion of strays is low (10-30%, Figures 8 and 9), it is a concern for two reasons:

  1. The number of adult spawners reaching the American River is lower.
  2. Hatchery strays can reduce the genetic integrity of the salmon population of the American River as well as other river populations, with unknown but potentially serious long-term consequences.

Straying occurs from Bay releases especially in dry years, because the hatchery smolts partially imprint on Mokelumne River water occurring at the release site near the mouth of the Napa River in eastern San Pablo Bay. Returning adults get mixed signals in late summer and early fall in the west Delta at the confluence of the Sacramento and San Joaquin rivers. Flows from both rivers have their signature at the confluence, because the Delta Cross Channel (DCC) is open all summer and early fall. Half the American River water can pass through the DCC and come out the San Joaquin channel. As a result, many American fish head up the San Joaquin channel and then up the Mokelumne forks.

Another theory is that because about a third of Mokelumne Hatchery smolt releases to the Delta and Bay wind up returning to the American River to spawn, their offspring are genetically coded to the Mokelumne.

What if?

What if more of the American hatchery smolts were released in the Bay or along the coast? That would increase returns about 50% in wet years (assuming all the returns were 2.5% in Figure 1) and more than double returns in dry years like 2016 (assuming all the returns were 1.25% in Figure 2.) Assuming conservatively that the hatchery contribution to the run is about 80-90 percent, the American fall-run salmon escapement of adults (Figure 10) would increase by over a third. A similar increase in fishery contributions from the American hatchery would also be likely. Since the American contributes about 20% to the overall Central Valley fall run escapement (Figures 10 and 11), Valley-wide contributions to fisheries and escapement would increase 5-10% with more Bay releases.

What if Delta outflow were increased in dry years in late spring during Bay hatchery smolt releases? That could increase dry year returns 50% or more (2015-2018 in Figure 10).

What if hatcheries only spawned their own river genetic coded adults and strays were removed on their way to spawning reaches? And what if Bay smolt releases were barged to Bay release sites instead of trucked? Such actions would reduce straying and improve the genetic integrity of each river’s populations.

What if hatchery smolts were not released in rivers? There might be less competition with wild smolts and reduced effects of predation and competition on wild steelhead fry that predominately emerge from redds in late spring.

Summary and Conclusion

The contribution of American River hatchery salmon smolts to adult spawner returns and fisheries would be significantly higher if these hatchery smolts were all trucked to the Bay. Straying to other Central Valley rivers would increase. However, competition with and predation on wild salmon and steelhead in the American River would decrease.

Figure 1. Percent survival (adult returns) of six tag groups of American River Hatchery releases of fall run salmon smolts in spring 2017. Data source: https://www.rmpc.org

Figure 2. Percent survival (adult returns) of six tag groups of American River Hatchery releases of fall run salmon smolts in spring 2016. Data source: https://www.rmpc.org

Figure 3. Comparison of 2016 and 2017 flows and water temperatures in spring.

Figure 4. Delta outflow in spring 2016 and 2017. Dots represent fall-run hatchery smolt releases. Blue outlined dots are river releases. Red outlined dots are Bay releases.

Figure 5. Sacramento River water temperature in the west Delta near Sherman Island in spring 2016.

Figure 6. North Bay water temperature near Bay hatchery salmon smolt release site in 2016.

Figure 7. Percent return of selected tagged hatchery smolt groups released to Bay by Delta outflow at the time of release with 2016 and 2017 noted. Data sources: https://www.rmpc.org and CDEC.

Figure 8. Returns of American River origin adult hatchery fall-run to four state hatcheries from 2016 drier year releases to river and Bay. Data source: https://www.rmpc.org

Figure 8. Returns of American River origin adult hatchery fall-run to four state hatcheries from 2016 drier year releases to river and Bay. Data source: https://www.rmpc.org

Figure 9. Returns of American River origin adult hatchery fall-run to four state hatcheries from 2017 wet year releases to river and Bay. Data source: https://www.rmpc.org

Figure 10. American River salmon escapement 1975-2019. Data source: https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=179102&inline=1

Figure 11. Central Valley escapement of four salmon runs 1975-2019. Note the fall run Chinook dominate. Data source: https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=179102&inline=1