Category Archives: Bay-Delta

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. ↩

Revised Delta Smelt Take Permit

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The Interior Department’s US Fish and Wildlife Service (USFWS) issued a memo1 on January 30, 2019 that revised the federal take permit for Delta smelt for the combined operation of the Central Valley Project and the State Water Project. The memo stated:

“It has become clear over the past several years that surveys are reaching their detection limits given the declining population of delta smelt, and in 2018, the FMWT [fall midwater trawl] Index was zero, indicating that the FMWT Index may no longer provide an accurate predictor of incidental take.”

The new take criteria are now the old action criteria of limiting Old and Middle River (OMR) reverse flows during the winter and spring under certain conditions. When smelt would normally be expected to be present, OMR flows would be restricted to being no more negative than -2000 or -5000 cfs. The new “surrogate” criteria essentially keep the south Delta pumping plant operations at status quo until such time as the ongoing reinitiated Endangered Species Act (ESA) consultation is completed and new take permits are issued.

The importance of the rule change is diminished by the fact that Interior (combined action of US Bureau of Reclamation and USFWS) has not enforced the rules to protect Delta smelt. The state of California has also failed to protect Delta smelt as well as California ESA-listed longfin smelt. One only has to review recent early winter information to see this is the case. After the first Delta outflow pulse at the beginning of December 2018, outflow fell to only 4000 through mid-December (Figure 1). High exports (Figure 2) contributed to the low outflow and exceptionally low (negative) OMR flows (Figure 3).

These low outflows and high exports created very high risk conditions for the two smelt species. What few Delta smelt remained were observed in the west Delta (Figure 4). Longfin smelt were spawning in Suisun Bay and the west Delta (Figures 5 and 6).

Smelt are not being protected. The Smelt Working Group mandated under the Federal and State take permits has been inactive and has not provided mandatory guidance. New take permits are needed immediately to protect the two listed smelts. The State Water Board, in revisiting water right permits and water quality standards for the Delta, should also adequately protect the listed smelts. To protect the smelts, the OMR limit for December should have been no more negative than -2000 cfs. The export-to-inflow limit criteria for December should be 35%, not the present 65%. December outflow minimums should be 6000-8000 cfs, not the present 3500-4500 cfs.

Figure 1. Delta outflow 11/10/18 to 1/8/19. Note very low outflow in early December after initial rainfall pulse.

Figure 2. State project exports at Clifton Court December 2018 to February 2019. Federal exports were near maximum (3500-4200 cfs) for most of period.

Figure 3. OMR flows November 2018 to January 2019.

Figure 4. December 2018 Kodiak trawl survey catch of Delta smelt.

Figure 5. December 2018 midwater trawl longfin smelt catch.

Figure 6. Smelt Larvae Survey #1 for 2019 catch of newly hatched longfin smelt.

Longfin Smelt February 2019

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In my last update on the status of longfin smelt (February 2018), I decried the continuing decline of the Bay-Delta population of longfin, which are listed under the California Endangered Species Act.  The fall index for 2018 indicates continued low population levels (Figures 1 and 2), with 10 to 100 times higher production in wetter years than dry years.  After the very poor recruitment in 2015 and 2016, there was some recovery in wetter years 2017 and 2018.  Despite record low spawner numbers in 2015 and 2016, recruits increased with wetter years 2017 and 2018, which in turn could lead to improvement in 2019 and beyond with indices above 100 (log 2.0 in figure 2) or perhaps even near 1000 (log 3.0 in figure 2).  If drought returns, bets are off.

Figure 1. Fall Midwater Trawl Index for longfin smelt, 1967-2018. Source: http://www.dfg.ca.gov/delta/data/fmwt/indices.asp

Figure 2. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. The relationship is very strong and highly statistically significant. Adding Delta outflow in winter-spring as a factor makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, lower-outflow years (red years). Data source: http://www.dfg.ca.gov/delta/data/fmwt/indices.asp.