Mokelumne Hatchery 2016-2018 Releases

In a post last year I remarked on the progressive management of the Mokelumne River hatchery. The hatchery is a mitigation hatchery operated by the California Department of Fish and Wildlife in partnership with the East Bay Municipal Utility District. Its activities over the past several decades have led to the recovery of Mokelumne River salmon.

The hatchery’s 6 million smolt releases continue to survive well under present management practices (Figures 1 and 2). Escapement of adults to the river and hatchery below Camanche Dam have numbered from 10,000 to 20,000 in recent years,1 a remarkable improvement given that they were produced during the 2012-2016 drought period.

The hatchery is still learning under its adaptive management program. The program has a diversity of release strategies that provide valuable information about the program and what works and what does not. Table 1 shows a summary of their smolt releases from 2016.

Table 1.  Summary of Mokelumne Hatchery smolt releases in spring 2016.  Source:

Release Date Release Location Smolts Released
4/20/16 Sherman West Delta 902,000
4/27/16 Sherman West Delta 470,000
5/05/16 Sherman West Delta 450,000
5/09/16 Mokelumne River 102,000
5/10/16 Golden Gate Bridge 202,000
5/12/16 Sherman West Delta 902,000
5/20/16 Sherman West Delta 920,000
5/25/16 Half Moon Bay (coast) 485,000
5/26/16 Mokelumne River 402,000
5/28/16 Sherman West Delta 915,000
6/03/16 Sherman West Delta 771,000
2016 Total 6,521,000

Returns from the 2015 spawn year (brood year 2015) from code-wire-tagged smolt groups released in below-normal/dry water year 2016 ranged from near zero to two percent (Figure 3). The half-million smolts released to the river had near zero returns to fisheries and river/hatchery, while the half-million releases to Half Moon Bay on the coast south of San Francisco had a good return of 2.2 percent. Returns from the remaining 5.5 million smolts released at Sherman Island in the west Delta ranged from 0.1 to 1.4 percent.

The wide-ranging survival rates provide clear guidance for future hatchery smolt-release management.

  • April releases do not fare as well as May releases, suggesting that the larger size of May smolts provides a survival advantage.
  • River releases in a below normal or dry year like 2016 have poor survival, especially with below average freshwater flows in the lower San Joaquin River (Figure 4) and low Delta outflow (Figure 5).
  • Releases at Sherman Island in the west Delta in early June had poor survival compared to May releases, coincident with rapidly falling flows (Figures 4 and 5) and rising water temperatures (Figure 6).

2017 and 2018 release strategies were similar, but weighted more heavily toward Bay and ocean releases.

  • Over one million smolts were released on the coast and at the Golden Gate in 2017; 730,000 in 2018.
  • Most of the 4 million smolts released at Sherman Island in 2017 were released in May.
  • Over 4 million smolts were released at Sherman Island in 2018 from mid-April to early June over a broad range of conditions.
  • Nearly 500,000 smolts were released in the Mokelumne River in 2017 and 2018. The 2017 smolts were released in June of a wet cool year, while the 2018 releases were in May of a drier, warmer year.2

If and when information on the tag returns from 2017 and 2018 releases becomes available, it may be possible to move toward a still more effective release strategy that increases smolt survival and contributions to fisheries and river escapement.

Figure 1. Escapement estimates to the Mokelumne Hatchery 1964-2018

Figure 2. Escapement estimates to the Mokelumne River 1952-2018.

Figure 3. Percent return of 2016 Mokelumne Hatchery tagged smolt releases. Source:

Figure 4. Inflow of San Joaquin River to the Delta in May 2016 along with long-term median flow.

Figure 5. Delta outflow in spring 2016.

Figure 6. Water temperature in lower San Joaquin River at Jersey Point in spring 2016.

  1. The American and Feather River escapement has been 20,000-30,000 and 40,000-60,000, respectively, for similar numbers of smolt releases.
  2. Note that San Joaquin River flows and Delta outflows are most important to Mokelumne Hatchery smolts, as the closure of the Delta Cross Channel results in the Mokelumne River being a tributary of the lower San Joaquin River.

Late-Fall-Run Salmon – Latest Update

In a January update on late-fall-run salmon, I noted record low runs of late-fall-run Chinook salmon to the upper Sacramento River in 2015 and 2016. That trend continued in 2017 (Figure 1), as shown in recent data published by the California Department of Fish and Wildlife.  Spawning runs from 2015-2017, the product of runs from the 2013-2015 drought, were three lowest since year 2000.

As it was for spawning run 2013, the rate of return for 2014 spawning run of tagged late-fall-run hatchery smolts was very low (Figure 2).  I concluded in the prior post that low river flows and lack of flow pulses caused the poor return rate.  There were flow pulses in winter 2014-15 (Figure 3).  However, only the later season release group responded strongly favorably to a flow pulse (Figure 4).  This  suggests that later winter releases of fish from the hatchery, in combination with flow pulses, provides higher rates of returns for hatchery fish.  Prescribed flow pulses from Shasta Reservoir in dry winters like 2014-15 (Figure 5) appear to improve survival of late-fall-run hatchery smolts.

Figure 1. Spawner-recruit relationship for late-fall–run salmon. Number is log10-3.5 transformed escapement (recruits) for the fall of that year. For example, year “16” represents escapement for late fall 2016, which includes spawners from early winter 2017. Spawners represent escapement from three years earlier (brood year). In the example, spawners for year 16 were the progeny of escapement in 2013. Colors represent winter rearing condition two years earlier. In the example, red “16” represents dry winter 2014. Green represents normal years two years earlier. Blue represents wet years two years earlier.

Figure 2. Hatchery smolt survival for brood years 2008-2013 based on coded-wire-tag returns.

Figure 3. Winter 2014-15 Sacramento River flows downstream of Battle Creek along with 50-yr average.

Figure 4. Return rates by date of release for late-fall-run tagged hatchery smolt release groups from winter 2014-15. Source:

Figure 5. Winter 2014-15 Sacramento River flows downstream of Shasta Dam along with 50-yr average. Note short term reservoir water releases in December and February prescribed to support upper river hatchery smolt outmigration.

Delta June 2019

Water year 2019 has been a very wet year.  Yet salmon and sturgeon survival was compromised by low flows and high water temperatures in the Sacramento River this spring.1 Young salmon survival has been further compromised by low flows, high exports, and high water temperatures in the Delta this past June.

Many of the wild smolts produced in Central Valley rivers this year entered the Delta in May and left (or died) by the end of June, as observed in Delta export salvage collections (Figure 1).  Many of the wild smolts captured in the south Delta likely originated from San Joaquin tributaries.  South Delta exports were near maximum at 10,000 cfs, about 70-80% of San Joaquin inflow to the Delta and 20% of total Delta inflow.  The high exports caused lower flows and associated high water temperatures (>20oC) in the Delta channel of the lower San Joaquin River (Figure 2), and contributed to similarly high temperatures in the lower Sacramento River channel (Figure 3).

The high Delta water temperatures (>20oC) compromised the survival of the salmon smolts in June.  Reducing the export limit to 5000-6000 cfs in June of this wet year would have kept the water temperature near a 20oC limit.  The water quality standards in the 1980’s and 1990’s under D-1485 had a 6,000 cfs June export limit.  In the past two decades under D-1641, the June export limit changed to 65% of total inflow.

New Delta water quality standards should provide export limits and inflow/outflow minimums that protect salmon through the spring months.

Figure 1. Chinook salmon salvage at south Delta export facilities in 2019. Note the prevalence of wild (non-hatchery) smolts in May-June.

Figure 2. Water temperature and tidally-filtered flow at Jersey Point in the lower San Joaquin River channel of the Delta in June 2019.

Figure 3. Water temperature and tidally-filtered flow at Rio Vista in the lower Sacramento River channel of the Delta in June 2019.



Sacramento River Salmon Opener Compromised

The California Department of Fish and Wildlife announced in May that the salmon season on the Sacramento River would commence below Red Bluff on July 16, with high expectations and expanded limits.

 “California’s inland salmon anglers can look forward to a better salmon fishing season than last year. A projected return of 379,600 spawning Sacramento River fall-run Chinook Salmon to Central Valley rivers has allowed fishery managers to return to a two salmon daily limit with four salmon in possession. This is a welcome increase over last year’s regulations, which restricted anglers to one salmon per day and two in possession.”

Yet despite near record water and a full Shasta Reservoir, the federal government is compromising the run with high water temperatures from low reservoir releases and high river diversions that violate state water quality regulations and water right permit requirements.

River flow near Red Bluff is just above 12,000 cfs (Figure 1), about 1000 cfs below average for this time of year.  River flow in the river a hundred miles downstream, upstream of the mouth of the Feather River, is just below 7000 cfs, also slightly below average (Figure 2).  The flow difference between the two locations reflects water deliveries to federal water contractors near 5000 cfs.

The high diversions and low flows result in high water temperatures in the lower river (Figure 3) that will compromise the fishery opener as well as survival and egg production of this fall’s spawning run.  The salmon run is already in a long-term decline (Figure 4) from poor water management and violations of standards and permits conditions.

Why allow the federal government to squeeze out more of California’s precious water and salmon?  Increasing Shasta releases or reducing diversions, or a combination thereof, by about 1000-2000 cfs should protect the migrating salmon and provide a better fishery opener.  With triple-digit weather forecasted for the latter half of July, it is imperative that river flows be increased.

Figure 1. Sacramento River flow near Red Bluff June-July 2019.

Figure 2. Sacramento River flow near Grimes at Wilkins Slough June-July 2019.

Figure 3. Sacramento River water temperature below Wilkins Slough June-July 2019. Note that water quality standard is 68oF, above which salmon become stressed.

Figure 4. Sacramento River fall-run salmon escapement 1952-2018.

Saving Killer Whales By Increasing Salmon Production

In a January 18, 2019 post, I related the state of Washington’s plan to increase the state’s hatchery salmon production to recover salmon populations and help the endangered southern population of killer whales.  In response to an executive order by the governor of Washington, the Washington Department of Fish and Wildlife’s proposed broad measures to increase the numbers of hatchery-raised salmon smolts released into killer whale migration areas that have minimal numbers of wild salmon.  The program would also enhance commercial and sport fisheries for salmon.  Much of the hatchery program would remain committed to recovery of threatened and endangered wild salmon stocks, which would also get a boost in essential habitat restoration.

The proposal in Washington state calls for an additional 30 million smolts for the Puget Sound estuaries (near Seattle) and an additional 20 million for the Columbia River estuaries, 50 and 20 percent increases, respectively.  The proposal recognizes:

 [H]atchery practices can pose serious genetic and ecological risks to wild populations if not managed carefully with full consideration of all that has been learned over the history of salmonid hatchery programs in the Pacific Northwest. However, the design of this proposal strives to minimize such negative impacts and to afford protection to the existing wild chinook populations to the greatest extent possible.

Elements of the program would include releasing hatchery smolts in lower river and estuary areas.  The program is designed to minimize effects on wild salmon by keeping these releases outside of the normal rearing and migration routes of wild salmon.  In some cases, hatchery salmon fry would be transported to net pens in lower rivers and estuaries for rearing and eventual release of smolts near the ocean, thereby further increasing smolt survival.  Returning adult salmon would home in on such sites, creating opportunities for terminal fisheries for hatchery salmon while retaining upriver spawning grounds for wild salmon.

A similar program is being planned and tested in California in the San Francisco Bay Estuary of the Sacramento and San Joaquin rivers.  Central Valley hatchery salmon smolts are already being trucked to the Bay and nearby coastal estuaries.  A new program element under consideration is the trucking of fry to local Bay estuary net pens for rearing.  If successful, this would create new terminal sport and commercial fisheries, while enhancing coastal fisheries and prey for the California Killer Whale populations.

One goal of the program in California would also be to shift hatchery salmon fisheries away from rearing areas and migration routes of wild salmon.  Rearing fry and releasing smolts in areas not frequented by wild salmon should reduce the effects of the hatchery program on wild salmon.  Similarly, terminal fisheries would focus harvest away from migration routes of wild salmon and reduce competition with wild salmon in spawning areas in upper rivers.  Commercial and sport fisheries would be enhanced along the coast.  New terminal fisheries would be created at estuary and coastal release sites that attract adults originally released at the sites as smolts.

If all goes well, such programs will benefit killer whales, sport and commercial fisheries, and wild salmon population (through reduced competition and better harvest management).

For more detail on Oregon and Washington Select Area Fisheries Enhancement programs see