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.

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.

Winter pulse flows benefit fall-run salmon fry by helping them emigrate to the Delta and Bay nursery areas (see discussion in February 2019 post). The tailwater spawning reaches of dams need reservoir releases to stimulate emigration of fry (Figure 1). Such releases piggy-back on stormwater flows in downstream tributaries, such as those in late January 2021 (Figure 2).

Nearly all Central Valley reservoirs are capturing recent high precipitation from their upper watersheds. With forecasts of further substantial rainfall into mid-February 2021, modest reservoir releases would provide substantial potential benefits to Central Valley salmon populations.

Figure 1. Sacramento River fall-run salmon fry catch near Red Bluff (river-mile 240) in winter 2020. Note that flow pulses stimulated winter fry emigration.

Figure 2. Flows from Shasta/Keswick reservoirs (river-mile 300, brown) and at downstream sites Bend Bridge (river-mile 250, green) and Wilkins Slough (river-mile 125, blue) in winter 2021. Note that tributary inflows created flow pulses in lower reaches of the Sacramento River.