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




Salmon and Sturgeon Compromised in Near-Record Water Year — June 2019

Lower Sacramento River water temperatures exceed water quality standards and lethal levels for newly hatched sturgeon.  In a prior post I discussed compromising water temperatures for sturgeon and salmon under low flows in dry years in the lower Sacramento River (see map, Figure 1).  But I did not expect the Bureau of Reclamation to violate its permit conditions for the Central Valley Project in this record setting wet year.  Flow in the lower river has dropped to 9000 cfs, and water temperature has risen above 20oC (68oF) at Wilkins Slough upstream of the mouth of the Feather River near Grimes (Figure 2; this is downstream of the area shown on the map).  In the week following June 10, Reclamation dropped reservoir release nearly 3000 cfs (Figure 3), leading to the rise in water temperatures.  The water temperature standard of 56oF was also exceeded in the upper river near Red Bluff (Figure 4).  The upper-river standard can be relaxed in drier years, but that would not apply in this near record wet year (Figures 5-8).

Figure 1. Map of the Sacramento River Basin (Princeton Ferry to Keswick Dam)

Figure 2. Water temperature and flow rate of Sacramento River at Wilkins Slough gage near Grimes. Water quality standard for lower river is 20oC (68oF).

Figure 3. Water release from Shasta/Keswick dams in June 2019.

Figure 4. Water temperature of upper Sacramento River near Red Bluff (RDB), Bend (BND), and Balls Ferry (BSF), May-June 2019. Red line is water quality standard for upper river.

Figure 5. Lake Shasta storage in 2019 compared to historical average, wettest, and driest years.

Figure 6. Lake Shasta water level and storage May-June 2019. Lake is at 98% capacity and 118% of average storage on June 15, 2019.

Figure 7. Snowpack in Central Valley December-July. Blue lines are 2019.

Figure 8. Mount Shasta on June 15, 2019.

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: .

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.