Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Water year 2021 is a bad year for American River wild salmon and steelhead production.

Water year 2021 has been bad for American River salmon and steelhead, with very low Folsom Reservoir releases Oct-Jan (Figure 1a).  Water year 2021 can best be described as a dry year, at least through the first quarter, somewhat on the drier side of 2018 and 2020, which were below normal water years.  However, whereas 2018 and 2020 followed wet years, water year 2021 follows a drier year.  This means 2021 started with poorer Folsom Reservoir storage (Figure 1b).

Water year 2021’s low fall and early winter reservoir releases from Folsom were nearer to 1000 cfs than the normal 2000 cfs.  As a result, much of the good spawning and early rearing fry habitat in the river below the dams remained dry (Figure 2).  In contrast, even in drought year 2014, the side channel spawning habitat remained slightly watered at 600 cfs river flow (Figure 3).  So, not only are redds dewatering in early winter of these dry years, the dewatering or drying of the side channels is getting worse.  This is either because the main channel is incising from persistent scouring or because sediment deposition blocks the entrance to the side channels, leaving perched side channels high and dry.

What got us into this predicament?  Was it simply Mother Nature or global warming?  Water management should take part of the blame (Figures 4 and 5).  The end-of-September Folsom storage in 2019 was higher than average at 700 TAF after a wet year.  Flood control rules required reservoir levels to be down to 600 TAF in November.  But storage dropped to 500 TAF, with higher-than-normal fall releases (Figure 6), essentially shorting the reservoir 100 TAF in the new 2020 water year.

The American River Water Forum Agreement Is designed to manage and protect all water users, including salmon.  Its formula for reservoir releases is based on natural flow input levels to the reservoir for that water year, which was lower than normal in 2020, thus leading to the prescribed low fall 2020 reservoir releases.  With reduced storage and low reservoir inflow in 2020, it was impractical to release the needed 2000 cfs for salmon and steelhead in fall 2020 without dropping the reservoir down to 200 TAF in what could be a drought year.

In conclusion, the American River salmon and steelhead are at the mercy of a precarious water management system that can go from good to bad in one water year.  One answer to this low fall flow problem is to ensure there is an extra 50-100 TAF of reservoir storage at the end of September to maintain the needed higher fall and winter flows for salmon and steelhead.  Because the channel morphology also continues to change, sediment supply and river morphology must also be taken into account, if not also adjusted.

Figure 1. Oct-Jan Folsom Reservoir releases 2017-2021 with long term average (above) and reservoir storage (below).

Figure 2. Sunrise side channel (looking upstream) end of January 2021 with some of the best spawning and rearing habitat for salmon and steelhead in the lower American River nearly dry with river flows at 1000 cfs. Other important side and main channel spawning and rearing habitats were similarly compromised. Note main channel is at extreme left middle of photo.

Figure 3. Sunrise side channel (looking downstream) on January 15, 2014. Some of the best spawning and rearing habitat for salmon and steelhead in the lower American River is in this side channel. In 2014 as shown, it was almost dry with river flows at 600 cfs. Note tops of salmon redds sticking out of the water in various stages of dewatering. The redds were dug by salmon earlier in fall 2013 at 1200 cfs.

Figure 4. Folsom Reservoir storage (acre-ft) in fall 2017-2020. Water years 2017 and 2019 were wet years, and water years 2018 and 2020 were below normal years.

Figure 5. Folsom Reservoir releases (cfs) in fall 2017-2020. Water years 2017 and 2019 were wet years, and water years 2018 and 2020 were below normal years.

Figure 6. Folsom Reservoir release (cfs) in fall 2019 with 64-year average.

Tisdale Weir Fish Passage Project

The California Department of Water Resources (DWR) Division of Flood Management is planning a major fish passage improvement to the Sutter Bypass: a notch in the Tisdale Weir.1 The notch will extend and enhance river flows into the bypasses, thereby allowing more access for juvenile salmon to rear in the bypass and improved upstream adult salmon passage from the bypasses back into the Sacramento River. DWR plans to place an operable gate in the notch, which DWR would open when flows over the weir ceased. This would extend the duration of flows into the bypass. As planned, DWR would not open the gate until after the weir had already overflowed.

In a May 2019 post I described similar improvements to fish passage into and out of the Yolo Bypass, including notches in the Fremont Weir at the upstream end of the Yolo Bypass where high flows in the Sacramento River overflow into it.

Potential Benefits:

Improving adult upstream passage and expanding rearing access to the bypasses with notch flows is a good concept. Improving rearing habitat in the bypasses is a further potential benefit. In wet years and in even in drier years (when the bypasses receive no Sacramento River overflows (or young salmon) even from the new notches), there will new potential benefits to tributary salmon populations (e.g., salmon from Butte Creek and the Feather and Yuba rivers). Sacramento River hatcheries can also improve their contributions by out-planting fry salmon to wetlands in the bypass. Managed wetlands in the bypass (including duck clubs and rice fields) can also be used for rearing wild and hatchery fry salmon, especially in drier years.

Potential Drawbacks:

More flow and access to the bypasses has the potential to put more salmon in harm’s way. More of the populations will rear and migrate in the bypasses. Stranding and predation in the bypasses are very real risks to young and adult salmon. Such risks need to be minimized. Rearing habitats need to drain effectively. Stranded young and adults should be rescued to the extent reasonably possible. There is a tendency in project plans and operations to ignore or downplay the stranding risks.

Further Needs:

There are multiple Sacramento River flood-control weirs that at times overflow into the Sutter Bypass and Butte Basin. These other weirs also need “fixing.” However, stranding (poor draining) in Butte Basin and Sutter Bypass will remain a serious problem, because hundreds of square miles of poor habitat conditions occur from top to bottom. Drainage and stranding need to be addressed before more access is provided. Information on smolt survival and run contribution from bypass rearing and passage is largely lacking.

Further Options:

Often the first major flow pulses in the Sacramento River bring the strongest downstream movements of young salmon (Figure 1). Proposed operation of the Tisdale Weir calls for the new gates to remain closed until after the weir overflows (Figure 2). This operation does not take advantage of a significant potential project benefit. For instance, had the new facilities been in place during the peak early-January fry emigration in wet year 2019 (Figure 1), the weir gates would have remained closed (lower graph in Figure 2) when they could have been opened prior to weir overflow on about January 12. The gates could also be opened in earlier pulses and more frequently in drier years like 2018 (top graph in Figure 2). Furthermore, early openings in wet and dry years would accommodate access to floodplain habitats for juvenile winter-run salmon (Figure 3). DWR would need to develop some forecasting and decision-making protocols to evaluate opening the new gates prior to overflows. But water already in the bypass from other sources could partly mitigate the juvenile stranding potential, and adults that had strayed into the bypass would have a better opportunity to escape.

Summary and Conclusions:

The Tisdale Weir Project could provide substantial benefits to Sacramento River salmon. However, the proposed operation does not address potential risks on the one hand and may not fully take advantage of potential benefits on the other hand.

Figure 1. Catch of fall-run-sized salmon in screw traps in lower Sacramento River near the Tisdale Weir in winter-spring 2019

Figure 2. Proposed operation (purple shaded) of Tisdale Weir gates under dry year 2018 and wet year 2019 water level conditions. Gates could be operated at flows above the green line. The weir would normally overflow at water levels in the Sacramento River above approximately 44-ft elevation.

Figure 3. Pre-smolt catch of winter-run-sized salmon in screw traps in lower Sacramento River near the Tisdale Weir in winter-spring 2019.

Sacramento River Salmon Redd Dewatering in Fall 2020

The Bureau of Reclamation’s standard fall operation of Shasta Reservoir and Keswick Reservoir dewaters the redds of fall-run Chinook salmon in the upper Sacramento River near Redding.  The peak in fall-run Chinook salmon spawning is October-November.  Eggs and alevin (hatched sac fry) remain buried one to two feet down in the gravel spawning bed (redd) for about three months.  As I described in a November 2019 post and in prior posts, drops in flow and associated water levels cause varying degrees of redd stranding or dewatering, and the affected eggs and alevins die.

Fall-run salmon spawn from September to December, with a peak in October-November.  It takes several months for eggs to hatch and fry to leave the gravel beds.  Under unregulated conditions, fall-run salmon spawn in the generally stable flows of fall, and their young move toward the ocean with winter rains.  The natural versus present managed flow patterns are compared in Figure 1.

The problem has been getting worse in recent decades with the greater emphasis on water deliveries and on summer spawning conditions for winter-run salmon.  Each fall, after the summer irrigation and the incubation period for winter-run Chinook salmon wind down, Reclamation reduces reservoir releases from Shasta and Keswick by 20-30%, especially in drier years like 2020 (Figure 2).  Water levels in 2020 dropped about 3 ft over the fall (Figure 3), completely dewatering the earliest redds.

Reclamation should have averted the problem by maintaining fall releases from Shasta near 5000 cfs (Figure 3), at a cost of about 100,000 acre-ft of Shasta storage for the fall, or about 5% of Shasta dry-year minimum storage (Figure 4).  The need would continue into early winter, but the effect on Shasta storage would depend on winter precipitation.

Figure 1. Managed vs full natural flow from Keswick Dam to the upper Sacramento River in fall 2020.

Figure 2. Keswick Dam water releases in 2020 and 57-year average.

Figure 3. Water levels in Sacramento River below Keswick Dam in 2020.

Figure 4. Shasta Reservoir storage in 2020. Note the reservoir had 1.3 million acre-ft of additional water stored at the beginning of the year than at the end. Water year 2019 was wet and 2020 was dry.

 

Butte Creek Spring Run Salmon – Status End-of-Year 2020

When I last reported in May 2017 on the status of Butte Creek spring-run Chinook salmon, the population had hit lows as a consequence of the 2013-2015 drought.  I am happy to report the run’s rebound after the drought with new reported and revised CDFW escapement estimates.

Following escapement in 2017 that was the lowest since 1998, the population estimate increased to 6253 in 2019 (Figure 1).  The spawner-recruit relationship (Figure 2) continues to indicate a positive spawner-recruit relationship, with and positive responses to normal water year 2016 in the 2018 run and to wet water year 2017 in the 2019 run.  Though 2018 was a below-normal water year like 2016, the run in 2020 produced by 2018 water conditions has been characterized as small.1 A small 2020 run may be the consequence of the low number of 2017 spawners.  In addition, the devastating 2018 Camp fire in the watershed may have adversely affected the 2020 adult returns and future spawning runs.  But overall, the outlook for the 2021 and 2022 runs is promising given the improved number of spawners in 2018 and 2019.

Figure 1. Butte Creek spring-run salmon escapement estimates, 1975-2019.

Figure 2. Spawner-recruit relationship of spring-run Chinook salmon for Butte Creek. Numbers shown represent recruits (number of returning adults) for year displayed. The color of the number shows the conditions two years previously, when young reared in Butte Creek and then emigrated to the ocean. A red number shows a dry year rearing and emigrating conditions. Blue designates wet year rearing and emigrating conditions. Green designates normal year rearing and emigrating conditions. For example, 17 represents escapement in 2017, while its red color designates drought conditions in 2015.

Tuolumne River Salmon Runs in Decline – End-of-Year 2020 Status

After decades of dominating the overall salmon run in the San Joaquin River watershed, the salmon run in the Tuolumne River now lags behind the runs in her sister rivers.  The Tuolumne River is a San Joaquin River tributary with no hatchery.  Its salmon runs are declining (Figure 1).  Unlike her sister rivers the Stanislaus and the Merced, the Tuolumne salmon run did not rebound as well after the 1987-1992, 2007-2009, and 2013-2015 droughts (Figure 2).

The Tuolumne run has had difficulty recovering from droughts because spawner numbers in subsequent years are too low.  There is a positive spawner-recruit relationship, heavily influenced by water year conditions (Figure 3).  Recruitment (run size) is influenced by the number of parent spawners (three years earlier), poor rearing year conditions (two years earlier), and poor conditions in the year adults return.. Runs from 1990-1992 had all three of these adverse conditions, which led to a 99% loss of their potential (two log levels).  The third years of the two recent droughts (2009 and 2015) had similar reduced potential, though with only two of the adverse conditions (poor rearing conditions and poor adult returns).

In a recent post, I related near-record-low salmon runs over the past several years in the Yuba River, a Sacramento River tributary that is similar to the Tuolumne in that it has no hatchery.  Like the Yuba, the Tuolumne salmon run is also markedly influenced by hatchery strays from other Central Valley rivers.  Hatchery strays from other rivers (Figure 4) dominate otherwise poor runs in the Tuolumne River in the years following droughts.  Many Battle Creek and Mokelumne River hatchery smolts trucked to the Bay in 2014-15 later strayed to the Tuolumne River to spawn.

Lack of returning wild salmon that are of Tuolumne River origin, and the dominance of hatchery strays after droughts, do not bode well for the native Tuolumne salmon run.  Resource agencies and other science experts have recommended maintaining a run of at least 500 native spawners for the run to remain “viable” (McClain 2010).  While recent runs since the 2013-15 drought have averaged near 1000 spawners, the fact that 60-70% are hatchery strays indicates that this goal has not been met over the past 15 years.  To increase wild salmon production, the State Water Board needs to adjust the allocation of Tuolumne River water, a process the State Water Board began in 2018.  Changes in the operation of the Delta pumps to reduce pumping during the emigration season would improve the success of all San Joaquin watershed salmon runs.  As native populations improve, river managers could reduce the influence of hatchery strays by ‘sorting out’ strays at the adult counting weir in the lower Tuolumne River; however, this would necessitate marking all Central Valley hatchery smolts.

Figure 1. Fall run Chinook escapement to the Tuolumne River 1975-2019. Data Source.

Figure 2. Fall-Run Chinook salmon escapement in San Joaquin River tributaries 1975-2019. Data Source.

Figure 3. Spawner-recruit relationship for Tuolumne River fall-run Chinook salmon. Numbers are log transformed minus 1 (2.00 = 1000). Numbers are recruits in their spawning return year. Red number is dry water year two years earlier when rearing as young. Red circle is dry year adult return year. Blue is wet year. Green is normal water year.

Figure 4. Source of hatchery strays in Tuolumne River spawning ground surveys in 2016 and 2017. Note only 25% of hatchery smolts are marked. Source.