Category Archives: Bay-Delta

Improved Yolo Bypass Fish Passage

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Some salmon and sturgeon adults migrating up the Sacramento River this spring have had new help in passing upstream via the Yolo Bypass. With roughly half the Sacramento River’s flood waters flowing through the Yolo Bypass at the beginning of March, many salmon and sturgeon returning to the upper river to spawn likely chose entered the lower end of the Bypass at Rio Vista. These fish had a new notch opening to help them get over the Fremont Weir at the upper end of the 40-mile-long Bypass (Figure 1) and back into the Sacramento River to continue their journey.

The new $6-million gated-notch opening in the Fremont Weir is the first of several to be built into the two-mile-wide weir to help fish passage. The notches will allow an easier passage route over the weir, especially for large sturgeon. The notches are especially important in allowing an extended period for adult fish to finish their passage through the Bypass when Sacramento River water levels fall and the river flow ceases spilling over the weir into the Bypass. In the past, these conditions would have trapped any fish that remained in the Bypass. The notches will also help pass downstream-migrating juvenile salmon to enter the Yolo Bypass, where there is potential beneficial tidal and floodplain rearing habitat.

The first year of the new notch’s operation has not been without some glitches.1 Significant numbers of salmon and sturgeon have died and probably continue to die at the weir and in the Bypass.

But the new notch was not the underlying cause of this problem. The problem lies in flood control and reservoir storage management in the Central Valley. Drastic reductions in river flow and water levels led to fish stranding in the Bypass, the draining of the floodplain, and a rapid rise in water temperatures in the Bypass that stressed migrating fish.

  1. Shasta/Keswick reservoir releases were reduced sharply after two major flood releases this winter/spring (Figure 2).
  2. This led to abrupt ends to Fremont Weir overflows into the Yolo Bypass (Figure 3)
  3. The sharp drops in water levels in the river allowed only one week of extended Bypass inflows through the new notch (Figure 4).
  4. That led to a rapid draining of the Bypass (Figures 5 and 6).
  5. This in turn led to excessive water temperatures in the Bypass (Figure 7) for migrating and rearing salmon (>70oF).

For the new notches to be effective, an extended period of flow through the new notches will be needed to allow time for migrating and rearing salmon and sturgeon to safely exit the Yolo Bypass without being subjected to a sudden draining of warm water from the shallow margins of the Bypass. With a near record snowpack and filling reservoirs, there were sufficient river flows and reservoir storage this year to extend the duration of river flows into the Yolo Bypass.

Figure 1. New Fremont Weir gated notch to help fish passage between Yolo Bypass and Sacramento River.

Figure 1. New Fremont Weir gated notch to help fish passage between Yolo Bypass and Sacramento River.

Figure 2. Reservoir releases from Shasta/Keswick dams in winter-spring 2019.

Figure 2. Reservoir releases from Shasta/Keswick dams in winter-spring 2019.

Figure 3. Flow into Yolo Bypass from Sacramento River at Fremont Weir in winter-spring 2019.

Figure 3. Flow into Yolo Bypass from Sacramento River at Fremont Weir in winter-spring 2019.

Figure 4. Water elevation of Sacramento River at Fremont Weir in winter-spring 2019. Top of weir is at 32-ft elevation. Bottom of new notch is at 25-ft elevation. Extended operation of new notch would have occurred from April 22-28.

Figure 4. Water elevation of Sacramento River at Fremont Weir in winter-spring 2019. Top of weir is at 32-ft elevation. Bottom of new notch is at 25-ft elevation. Extended operation of new notch would have occurred from April 22-28.

Figure 5. Flow in upper Yolo Bypass in winter-spring 2019.

Figure 5. Flow in upper Yolo Bypass in winter-spring 2019.

Figure 6. Water elevation in mid Yolo Bypass during Bypass draining in last week of April 2019.

Figure 6. Water elevation in mid Yolo Bypass during Bypass draining in last week of April 2019.

Figure 7. Water temperature in mid Yolo Bypass at Lisbon Weir during Bypass draining in last week of April 2019.

Figure 7. Water temperature in mid Yolo Bypass at Lisbon Weir during Bypass draining in last week of April 2019.

 

South Delta Salmon Trap

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Unless there are high Delta inflows, south Delta export pumping creates a hydrologic “trap” for emigrating salmon and other Delta fishes. Even under moderate Delta inflows and outflows, as occurred in January 2019 (Figure 1), south Delta pumping traps salmon emigrating from both the Sacramento and San Joaquin river systems. This is because the pumps trap nearly all the water from the San Joaquin and about a third of the Sacramento River water the latter primarily via cross-Delta flow in Georgianna Slough (GS). In contrast, under high flows, the trap is confined only to the immediate area of the south Delta export pumps (Figure 2).

Susceptibility to the “trap” for Sacramento salmon under moderate early winter Delta flows is evident from the collection of smolts from the Coleman fish hatchery at south Delta fish salvage facilities (Figure 3, blue and green dots). Susceptibility of San Joaquin salmon smolts under moderate and high flows is evident from San Joaquin hatchery smolts salvage (Figure 3, orange dots).

Lower export limits in winter-spring since 2009 have helped to minimize the frequency of conditions in which salmon become trapped in the south Delta. Exports and salmon salvage are 30-50 % lower than pre-2009 levels, and sometimes lower still. However, political forces may eliminate these export restrictions and greatly increase the trapping of salmon in the south Delta. This would further limit the potential for salmon recovery in the Central Valley.

The State Water Board’s ongoing process of setting new Delta water quality standards should adopt more stringent measures to minimize the trapping of salmon in the south Delta. Such measures should include further restrictions on exports and increased flows in the lower San Joaquin River. Other options include:

  1. Constructing a barrier or fish screen at the head of Old River;
  2. Opening the Delta Cross Channel to increase net downstream flows in the lower San Joaquin channel within the Delta; and
  3. Increasing Delta outflow.

Figure 1. Delta hydrology 1-15-19. Red arrows denote negative or upstream flows. SR = Sac River. JPT = Jersey Point. GS = Georgianna Sl. MOK = Mokelumne River. DS and FR = Dutch Sl and False River. PPT = Prisoners Pt. OMR = Old and Middle Rivers.

 

Figure 2. Delta hydrology 3-15-19. Red arrows denote negative or upstream flows. SR = Sac River. JPT = Jersey Point. GS = Georgianna Sl. DS and FR = Dutch Sl and False River. PPT = Prisoners Pt. OMR = Old and Middle Rivers.

Figure 3. Salmon salvage in winter-spring 2019. Colored dots represent specific hatchery release groups noted by date of release along top margin of chart. River and Delta flows and exports (SWP+CVP) are shown in bottom chart.

Dutch Slough Tidal Marsh Restoration

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The Dutch Slough Tidal Restoration Project,1 newly redesigned (Figure 1), has some improved design elements, but remains flawed and potentially detrimental to Delta native fishes. Unless the flaws are overcome, the project will be a huge waste of limited Delta restoration funds.

First, the proposed project’s location within the Delta (Figure 2) is extremely detrimental.

  1. The location is an eastward extension of Big Break, an open water of the west Delta that is infested with non-native invasive aquatic plants and that breeds non-native fishes.
  2. The project is located on Dutch Slough, detrimentally warm in summer (Figure 3), with net flows that are negative and eastward toward the south Delta export pumps (Figure 4).

Second, and equally important, the project as designed would further contribute to the existing detrimental non-native vegetation and warm water problems.

  1. The extensive new dead-end slough complexes will become infested with invasive plants and will contribute to lowering turbidity and warming.
  2. The new subtidal habitat will further add to that in Big Break with more invasive plants and breeding and rearing habitat for non-native fish.

Third, the new habitat will attract breeding smelt and rearing juvenile salmon into an area where their eventual survival is highly questionable.

Can design changes overcome these flaws? Yes, but only in combination with other regional fixes.

  1. Big Break must first be restored along the lines being considered and studied in the Franks Tract Restoration Feasibility Study.
  2. A tide gate must be installed on east Dutch Slough, similar to that being considered for False River in the Franks Tract restoration. (This would fix the negative net flows toward south Delta exports and reduce salinity intrusion.)
  3. Open-water subtidal habitat should be eliminated. (Make the subtidal element diked-off non-tidal marsh.)
  4. Dead-end sloughs should allow flow-through to increase tidal circulation.
  5. Finally, more freshwater outflow should be allocated by reducing south Delta exports in low outflow conditions, in order to reduce salinity intrusion.

Figure 1. Conceptual design of Dutch Slough restoration project.

Figure 2. Location of Dutch Slough Project in the Delta.

Figure 3. Water temperature in Dutch Slough in 2014 and 2015.

Figure 4. Daily net flows in Dutch Slough 2007-2018.

 

 

The Importance of the Bay-Delta Estuary to the Recovery of Wild Chinook Salmon

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Common sense says salmon recovery efforts should focus on the most important factors that control fish population dynamics. In reviewing Central Valley population dynamics, I have seen each life stage and each individual controlling factor become important at one time or another. In my experience, the estuarine rearing and migrating stage is an essential component that is not given enough attention.

Central Valley salmon populations are nearly all “ocean-type” Chinook salmon, meaning they move to the ocean usually during their first six months of life, with substantial estuary rearing as fry, fingerlings, and pre-smolts. That is not to say that yearling smolts contributions are not important. It is that they are a minor contribution in “ocean-type” Chinook (note that late-fall-run are “river-type”).

I have always believed the survival of wild salmon fry in the Bay-Delta to be a key limiting factor in wild salmon production in the Central Valley. Hatcheries have kept smolt numbers to the ocean up, while the survival of wild salmon eggs, fry, fingerlings, and smolts has worsened. Fry-fingerling estuary survival is important, if only in the sense of sheer numbers and the resulting potential to increase overall smolt production. This is true for fall-run, spring-run, and winter-run populations. There is substantial evidence that returning wild adult salmon are predominantly from the estuarine-reared groups. Such evidence exists from fish surveys, scale analyses, and genetic studies. Thus, a recovery program for wild salmon should include a strong focus on estuarine rearing and survival.

My beliefs are shaped in large part from my personal experiences in conducting winter seine and screw trap surveys throughout the Bay-Delta and lower rivers. Young wild salmon classified as fry and fingerlings, 30-50 mm (1-2 inches), dominate the inshore landscape and screw trap collections. Millions of fry and fingerlings pour out of the spawning rivers and tributaries into the main rivers and into the Delta, where they dominate the winter fish community. Larger, more elusive pre-smolts, mostly winter-run, are also present in smaller numbers, but in numbers important to the winter-run population. Yes, there are millions of fry left to rear in highly regulated and disturbed river habitat, but their overall numbers are fewer, with less potential for ultimate survival to smolts entering the ocean than their estuarine counterparts.

One of the better indicators of the general pattern of estuarine use by salmon is fish salvage collections at the massive federal and state pumping plants in the south Delta. As shown in Figure 1, December is important in the estuary for winter-run and late-fall-run pre-smolts and yearlings, respectively. The January through March period is important for spring-run and fall-run fry/fingerlings. The April through June spring period is important for spring-run and fall-run pre-smolts.

To support juvenile salmon in the estuary, Delta habitat therefore needs protection from December through June. Natural flows and flow direction patterns are important habitat features. Water temperature is important in late spring. Exports affect such habitat, especially in dry, low-flow years.

The State Water Resources Control Board is in the process of revising water quality standards in the Bay-Delta watershed.1 Salinity, flow, water temperature, and export-limit standards need updates to protect salmon using the Bay-Delta through the winter and spring. Such protections will be key to wild salmon recovery in the Central Valley.

Figure 1. Salmon salvage at south Delta pumping plants in 2011. Note red-outlined groups of predominately wild salmon. Blue dots depict salvage events for hatchery salmon.

 

The Delta’s Trophic Collapse Explained

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A just-released UC Davis Study1 concludes that the decline in the Delta pelagic open water habitat and fishes is strongly related to non-native clam invasions and water exports. This long-held theory now has strong supporting evidence.

“The low pelagic productivity of the SFE [San Francisco Estuary] is considered a primary cause for the low abundance of several resident fish species (Sommer et al. 2007), including the imperiled Delta Smelt (Feyrer et al. 2003; Sommer et al. 2007; Hammock et al. 2017; Hamilton and Murphy 2018).”

In their study paper, the authors reviewed five theories on the decline in estuary productivity:

  1. Grazing by invasive clams.
  2. Ammonia inhibition from sewage treatment plants.
  3. Phosphorus limitation
  4. Elevated nitrogen.
  5. Freshwater exports.

The paper concludes there is “a growing consensus that the decline in pelagic fish abundance in the SFE is at least partially due to a trophic cascade, triggered by declining phytoplankton (Feyrer et al. 2003; Sommer et al. 2007; Hammock et al. 2017; Hamilton and Murphy 2018)”.

The authors noted that “the suppression of phytoplankton abundance due to exports cannot be reversed with equivalent releases from upstream reservoirs. Releasing water in late summer/fall increases flow, which decreases residence time, and therefore suppresses phytoplankton abundance (Table 2, Fig. 6).” This finding is extremely important because the primary form of mitigation for Delta exports has been maintaining outflow by increasing inflow with reservoir releases.

The study’s analyses strongly indicate that the decline in estuary productivity is associated with the clam invasion and increasing exports over the past five decades. The effects are most pronounced in non-wet years when fish production is most negatively affected.

There are factors not discussed in the study paper that deserve mention:

  • The increase in invasive clams and the more upstream distribution of clams are also enhanced by the increasing exports and lower Delta outflows resulting from higher exports.
  • The reduction in zooplankton (fish food) and fish abundance is also directly affected by the entrainment of both in exports.
  • The trophic collapse is also related to an increase in invasive rooted and floating aquatic plants, including Egeria and hyacinth over the same period. These plants compete with phytoplankton for nutrients and pelagic habitat. They also mechanically trap phytoplankton. For example, when flood tides carry turbid phytoplankton and water laden with suspended sediment into margin habitats that have an abundance of aquatic plants, ebb tides return clear water. Invasive aquatic plants have also benefitted from declining phytoplankton and suspended sediment, setting off a vicious circle of declining pelagic productivity.

 

  1. Hydrodynamic Modeling Coupled with Long-term Field Data Provide Evidence for Suppression of Phytoplankton by Invasive Clams and Freshwater Exports in the San Francisco Estuary, April 8, 2019. See description (“Clams and Water Pumping Explain Phytoplankton Decline in San Francisco Estuary” at: https://www.ucdavis.edu/news/clams-and-water-pumping-explain-phytoplankton-decline-san-francisco-estuary. ↩