Category Archives: Bay-Delta

Cache Slough Tidal Wetland Restoration – Update More misguided resource-damaging habitat restoration for an already highly altered and compromised Delta

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Cache Slough Complex Restoration

The Cache Slough Complex is in the lower (southern) Yolo Bypass in the north Delta region (Figure 1). It is the focus of the state’s tidal wetland restoration EcoRestore Program that spans 16,000 acres in the Cache Slough region of the Sacramento-San Joaquin Delta.

The 53,000-acre Cache Slough Complex is located in the northwest corner of the Sacramento-San Joaquin River Delta in Solano and Yolo counties (Figure 1). The Yolo Bypass receives inflow directly from the Sacramento River (Fremont Weir), the Colusa Basin Drain, Putah and Cache creeks, and agricultural and municipal discharges. The Cache Slough Complex exits the Yolo Bypass via Cache Slough, first connecting to the outlets of Miner and Steamboat Sloughs, before entering the tidal Sacramento River channel near Rio Vista.

The Cache Slough Complex has been identified as an area with great potential for tidal restoration as a result of its connectivity with the Yolo Bypass floodplain, suitable elevations, high turbidity, high primary and secondary productivity, and use by Delta smelt (Hypomesus transpacificus), Chinook salmon (Oncorhynchus tshawytscha), and other native fishes. Both federal and state wildlife agencies consider the Cache Slough Complex to be a prime area to advance habitat conservation to benefit endangered species in the Sacramento-San Joaquin Delta and incorporate improvements to the regional flood management system.

The latest project approved for construction is the Lookout Slough Project, a 3000-acre tidal marsh restoration immediately to the west of Liberty Island. The Project was certified by DWR in 2020 as mitigation/compensation for the Delta Tunnel Project. The Delta Stewardship Council recently denied appeals1 to the state’s certification of the Lookout Slough tidal marsh restoration project. Once completed, Lookout Slough will be the Delta’s largest single tidal habitat restoration project to date.

The Problem

Most of the tidal “restoration projects” in the Cache Slough Complex involve breeching leveed tracts of agricultural land to create subtidal or intertidal habitat. Tidal waters once confined to narrow floodplain channel are now allowed to pour through breaches onto over 10,000 acres of formerly diked farmlands. The process started between 1980 and 2000 when Little Holland Tract (1456 acres) and Liberty Island (4340 acres) levees failed and were not repaired, leaving these lands open to the tides. Because these reclaimed wetlands had subsided during active farming, most of the “restored tidelands” became sub-tidal, year-round, warm, shallow, open-water habitat. Such habitat is too warm for Delta native fishes except during the winter.

The enhanced tidal exchange and warm productive winter and early-spring habitat attracts migratory Delta native fishes like smelt, splittail, and salmon to the Cache Slough Complex. While such habitat is considered beneficial in winter, it warms excessively in spring and summer, reducing the period of quality rearing, and can reduce overall survival and production. Native fishes have succumbed to the heat, stranding in the uneven landforms, and predation by non-native warm-water fish.

The latest projects, Lower Yolo Ranch (1749 acres), Yolo Flyway Farms (300 acres), and Lookout Slough (3000 acres), will add 5000 acres of mostly shallow intertidal habitat. Tidewater will flood onto these lands twice a day to warm in the California sun and then return to cooler deep, shaded, sub-tidal sloughs long considered prime Delta smelt and salmon rearing habitat. Not only will the new inter-tidal “wetlands” be too warm, but they will contribute to warming adjacent sub-tidal sloughs that convey water to and from other parts of the north Delta. This water quality degradation gets worse with each new project and has resulted in the degradation of the entire north Delta as a viable spawning, rearing, and critical habitat of Delta smelt. The effect has measurably contributed to the near extinction of Delta smelt.

The Evidence

The United States Geological Service has many water quality and flow monitoring gages in the Cache Slough Complex (Figure 2) that provide considerable evidence of the above-described problem. Specific gages with pertinent data records reviewed for this post are highlighted in Figure 2.

Waters in the northern Cache Slough Complex become too warm for salmon and smelt (>20ºC) by spring (Figure 3). In summer (Figure 4), water tidally flooded into subtidal island-tracts can warm 5-7ºC over a day before draining back into adjacent sloughs. Water temperatures in the northern sloughs of the Cache Slough Complex reach 25ºC (lethal to smelt) or higher in summer, even in wet and normal water years (2016-2018, Figure 5). Water temperatures in the southern Cache Slough Complex are only slightly lower (Figure 6). Over the past decade, water temperatures in the Cache Slough Complex overall have been gradually increasing (Figures 7 and 8), to the detriment of Delta native fishes.

The Solution

The problem can be lessened or even reversed at existing and future restoration projects by:

  1. Limiting tidal access to sub-tidal sites to winter, when water and air temperatures are colder.
  2. Building projects with flow-through tidal channel features rather than a single opening.
  3. Ensuring that projects are inter-tidal with small, narrow, shaded channels, or tule benches.
  4. Narrowing, deepening, and shading connecting tidal sloughs.
  5. Limiting discharge of warm agricultural wastewater into tidal channels.
  6. Providing supplementary inflow of Sacramento River water from the Fremont Weir, from the entrance gates of the Sacramento Deepwater Shipping Channel, or from other locations.
  7. Retrofitting existing restoration sites and designing future projects as outlined above.

 

Figure 2. USGS gage locations in the Cache Slough Complex.

Figure 3. Water temperatures recorded at Little Holland Tract in 2015-16.

Figure 4. Water temperatures and water surface elevation (gage height) recorded at Little Holland Tract in July 2017. Note higher water temperature spikes occurred with strongest ebb (draining) tides.

Figure 5. Water temperature in Liberty Cut adjacent to Little Holland Tract, 2016-18.

Figure 6. Water temperature and tidally-filtered flow rate in Sacramento Deepwater Ship Channel, April-September 2021.

Figure 7. Water temperature in lower Cache Slough, 2011-2016.

Figure 8. Water temperature in the lower Sacramento River channel near Rio Vista, 2010-2019.

Yolo Flyway Farms Tidal Wetland Restoration Project

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Yolo Flyway Farms

The Yolo Flyway Farms project is a new element of the state’s EcoRestore program to fulfill requirements of federal biological opinions for the State Water Project and Central Valley Project. The 300-acre tidal wetland restoration project is located in the southern Yolo Bypass in what is commonly referred to as the Cache Slough Complex (Figure 1). The Project’s design entails allowing tidal access to excavated upland irrigated pasture land by opening levees along Prospect Slough (Figure 2). The Project is in a known area of concentration for Delta smelt as determined by nearby CDWR screw trap sampling in Prospect Slough (Figure 3). Project sponsors submitted a certification of consistency with the Delta Plan to the Delta Stewardship Council.1

Are such projects in the best interest of the Delta smelt population? A close look at project attributes may help answer the question.

Positive attributes:

  1. Replacement of the existing tide gate irrigation system with open levee breaches eliminates existing entrainment and loss of Delta smelt and other fishes into the irrigated pasture lands.
  2. New tidal channels and tidal wetlands would provide rearing habitat for young smelt, salmon, and splittail. Plankton and benthic invertebrate food sources for fish would likely increase.
  3. Hard surfaces may provide smelt spawning habitat.

Negative attributes:

  1. Tidal channels would provide new habitat for predatory birds and fish , which could increase loss of young smelt and salmon. Prospect Slough is deep, turbid, strong- current habitat unfavorable to predators. Tidal channels of project would be dead end, low velocity, less turbid habitats favorable to predators of fish.
  2. The southern Yolo Bypass aquatic habitats are warm from spring through fall, at times exceeding the thermal optimum for Delta smelt. Proposed shallow-water dead-end sloughs and flooded wetlands would warm and increase warming of Prospect Slough and other lower Bypass waters. While a positive attribute in winter and at times in late fall and early spring, this would be detrimental at other times.

Despite the potential positive benefits of such restoration in general, the potential negative aspects of the Project are a real concern. Some of the potential negative effects could be reduced through changes in project design and operations. At a minimum, the project should be considered an adaptive management experiment where potential positive and negative attributes are studied to determine the overall benefit of the action and whether it fulfills the objectives of the biological opinions.

Figure 1. Yolo Flyway Farms Project location (red circle) in southern Yolo Bypass.

Figure 3. Prospect Slough adjacent to Deepwater Shipping Channel and Liberty Island in southern Yolo Bypass. CDWR screw trap in yellow circle.

NOAA Advocacy under ESA

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On March 31, 2022, the Delta Independent Science Board (ISB) met to discuss: “How the State Water Project and Central Valley Project comply with the Endangered Species Act.”  Cathy Marcinkevage, Assistant Regional Administrator in the California Central Valley Office of the National Oceanic and Atmospheric Administration, NOAA Fisheries division, provided an overview of the federal Endangered Species Act (ESA) and the ESA Section 7 consultation process between NOAA and the Bureau of Reclamation regarding the effects of the Central Valley Project (CVP).

During questions, the ISB’s Dr. Robert Naiman asked if NOAA has “…the legal clout to require dams and other water diversions to install fish passage facilities.”  He provided context, observing: “…[N]one of the dams within the Delta’s watershed have fish passage facilities, and yet you have endangered species that could use the habitat above the dam, assuming you can get them through…” Naiman also noted: “In the Pacific Northwest and elsewhere, there have been a lot of retrofits for fish passage facilities as well as retrofits for regulating water temperatures in the rivers.”

In response, Ms. Marcinkevage spoke to NOAA’s authorities pertaining to fish passage at CVP dams.

First, she mentioned NOAA’s technical criteria for fish passage at intakes at diversion dams’ structures, for example the specifications along the surface of a fish screen: “We do have passage criteria for projects in terms of sweeping velocity and things like that.”

Second, she identified NOAA’s authorities under the Federal Power Act to prescribe fish passage at hydropower facilities (which all major Central Valley dams have).  However, this law does not pertain to federal dams, including the CVP dams.

Third, she said that NOAA, under the Federal Endangered Species Act (ESA), can be an advocate during ESA consultation with federal agencies: “With Section 7, we can try to advocate and get projects to do things within our needs.” [Emphasis added]

This is where we take issue with Ms. Marcinkevage.  Under the ESA, NOAA is clearly more than an advocate.  The agency has the principal regulatory authorities and responsibilities to protect and recover ESA-listed anadromous fishes.

NOAA’s job in a Section 7 consultation includes analysis of a project (action) as proposed, which Ms. Marcinkevage described: “But our job there is to analyze the project as it has come to us and identify its likelihood of jeopardizing the species.”  However, the ESA consultation process often also requires changing the details of the proposed project if necessary so that the project complies with the ESA.

Furthermore, NOAA must analyze the effects of a proposed action in the much broader context of the past and present baseline effects, to which a proposed action’s effects are added.  The baseline geographic reach and scale of the CVP are vast.  The CVP was and continues to be a major source of “stressors” that led to the ESA listing of multiple salmon, steelhead, sturgeon, and smelt species, including most of California’s anadromous fishes.

In addition to the large-scale hydrologic influences exerted downstream of the CVP impoundments, CVP dams were constructed with no fish passage facilities.  As a result, part of the CVP baseline is complete blockage of anadromous fish for decades, extending to the present.  Without access, vast amounts of habitat capacity and habitat diversity of anadromous fishes have been lost.

Dr. Naiman noted that endangered fishes could potentially use the habitat above the dams. Dams constructed with no fish passage are not unique to California, and the biological consequences they impose are well understood.  Salmon populations blocked from their historical habitat suffer devastating losses of abundance, productivity, and spatial diversity. These well-known facts were most likely what prompted Dr. Naiman’s question about NOAA’s legal authorities to require fish passage.

The ISB can and should be asking if it is possible to recover the salmon populations by “fixing” rim dam infrastructure and operations, and lower river and Bay-Delta habitats and water diversions, without fish passage past rim dams.  Stated another way, is recovery even possible in the absence of restored passage to historical anadromous habitats above the dams?

Ms. Marcinkevage suggested that NOAA can “work out” with the action agency alternatives to a proposed action that blocks or impairs fish passage:

“Now, as we do that [analyze the project], if we were to find that this project will continue to be a barrier or impose a barrier that will impede passage, we could work out an alternative that would prevent that.”

To date, nowhere in California’s Central Valley has NOAA performed an evaluation of a dam, found it to be a barrier to anadromous fish passage, and worked out a solution to the blockage of fish migration.  As Dr. Naiman observed, none of the major dams within the Delta’s watershed provide fish passage.

Clearly, NOAA has ESA authority to require alternatives to avoid jeopardy.  Exercise of this authority gets closer to Dr. Naiman’s question about the agency’s “legal clout” to require fish passage facilities.  Ms. Marcinkevage’s response did not differentiate between reasonable and prudent measures (RPMs), and reasonable and prudent alternatives (RPAs) in an ESA biological opinion.  RPMs are voluntary on the part of the action agency, while RPAs are NOAA-enforceable, and could include fish passage requirements.

Ms. Marcinkevage expressed a frank opinion about how to go about creating fish passage over CVP dams:

“But there’s something to not wanting to come in and being the completely authoritarian with the heavy regulatory hand to impose something that, frankly, can’t be done, but rather work out a more workable solution.”

Has NOAA concluded that passage over the CVP dams can’t be done?  The 2009 salmon Biological Opinion for the CVP included an RPA that required fish passage at Shasta and Folsom reservoirs.  It was that requirement that leveraged NOAA, in 2017, to conduct a test in Shasta Reservoir.  The test released juvenile salmon in the McCloud Arm to understand their ability to transit Shasta Reservoir during a wet water-year’s higher flows.   ~70% of the test fish reached the Dam.  A much lower transit success (~1%) occurred in a second experiment undertaken during an average water-year.  These are hardly unexpected results, given the enormity of Lake Shasta.  In order to capture emigrating juvenile salmon with high efficiency, head-of-reservoir collectors (rather than collectors at the dams) are sometimes deployed in Pacific Northwest reservoirs, although the reservoirs are much smaller than Shasta.

In 2019, the Trump administration stopped NOAA’s fish passage efforts at Shasta in their tracks.  The bogus Trump 2019 BiOp for the CVP eliminated the RPA that required fish passage.  And Trump’s Forest Service administrators ordered NOAA to not use Forest Service land for fish passage actions.  Now, NOAA will be conducting further studies in 2022 or 2023 to evaluate head-of-reservoir collection of downstream-migrating juveniles where the McCloud River enters Shasta Reservoir.  Though these studies are as yet voluntary, there is a fair likelihood that the forthcoming new salmon Biological Opinion will restore the fish passage RPA.

Notwithstanding NOAA’s preference to avoid a “heavy regulatory hand” under its ESA authority, the agency is entrusted with legal responsibilities to protect and recover listed species.  Enacting “collaborative,” less controversial mitigation alternatives at Battle Creek led to 20 years of delay in removing, or putting fish ladders over, only some of the small hydropower dams on Battle Creek that PG&E has now decided to abandon.  And in any case, recovering listed Central Valley salmon species without fish passage to major watersheds upstream of Central Valley rim dams is unlikely.

NOAA’s Recovery Plan for ESA-listed Central Valley salmon calls for at least three viable and spatially-diverse winter-run Chinook populations to recover the species.  If that’s to be accomplished, fish passage investigations at Shasta Dam need to be carried out and completed with haste.  The alternative is for the public to enlist the judicial system to provide the “heavy hand” needed for effective application of the ESA to protect our public trust resources.

American Shad – It is time to manage their populations

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I have studied American shad, a popular sportfish and anadromous herring native to the East Coast, in the Hudson, Columbia, Sacramento, American, Feather, Yuba, and Stanislaus rivers. I have also fished for them for 50 years.  They are the most abundant anadromous fish in the Bay-Delta and Columbia River watersheds.  Millions run up the Sacramento and Columbia rivers every spring to spawn.  The 1-to-6-pound adults arrive in spring and spawn from late spring into summer as waters warm.  After spawning, some die, but many adults return to the ocean.   The eggs are large like those of salmon, but. unlike salmon eggs, shad eggs float and hatch as they drift downstream toward tidewater in the Delta through late spring and summer.  Young shad then rear in the tidal estuary through the summer before heading to the ocean.

Shad interact with our native fish in various ways, most of which are detrimental.  Whether they and other nonnative fish like striped bass contribute to population declines of native species like salmon, steelhead, smelt, and sturgeon is open to debate.  I believe that coupled with changes in climate and water management, the effects of nonnative fish on native species are getting worse.

A 2017 review of the ecological role of American shad in the Columbia River (Haskell 2017) provided three hypotheses regarding the Shad’s effect on Columbia River food webs:

  1. Juvenile shad are an abundant and highly energetic food that increase the growth rate of major salmon predators [e.g. Northern Pikeminnow, Walleye, Smallmouth Bass, and Channel Catfish) – viewed as negative by supporting production of salmon predators.
  2. Juvenile shad are planktivores that compete with juvenile salmon, particularly later migrating sub-yearling Chinook Salmon in the lower Columbia River – viewed as negative by reducing food for salmon thus reducing growth and survival.
  3. Large numbers of adult shad could influence nutrient balances given their capacity to convey marine-derived nutrients – another source of marine carbon input viewed as positive.

I would add four further hypotheses/issues on the role played by American shad:

  1. Adult shad migrate from the ocean into the Bay-Delta estuary in spring on their way to spawning rivers. They number in the millions, feeding on plankton including larval fish such as newly hatched Longfin and Delta smelt, and fry salmon that frequent the estuary and lower rivers.
  2. Adult shad spend late spring and most of the summer spawning in major in the mainstem rivers and their larger tributaries, during which they feed on aquatic invertebrates and juvenile salmonids. Their spawning run in the spring coincides with the rearing of juvenile fall-run salmon and steelhead.  Shad adults can be extremely abundant during the spring emergence of fry steelhead, especially in tailwaters below dams that block shad migrations.  The American, Feather, Yuba, and Mokelumne Rivers have such conditions.  Historical anecdotes of adult shad feeding on young salmonids below the Red Bluff Diversion Dam in the upper Sacramento River are available from CDFW predator survey reports.  In my own experience, I commonly use small spoons representing salmonid fry and parr size (2-3 inches long) that are readily swallowed by feeding adult shad.
  3. Adult shad may spawn through the summer in some tributary tailwaters where cold water releases (<65ºF) are prescribed for over-summering salmonids. Cold water can extend the period of shad spawning and the period in the tidal estuary when juvenile shad compete with smelt and other fishes for zooplankton prey.
  4. Juvenile American shad rear in freshwater and low-salinity tidal zones of the Bay-Delta estuary from late spring through summer (Figures 1-6), where they feed on zooplankton of the same types as Delta smelt and other native fishes.

As is the case with many native fish species, American shad populations suffer during periods of drought.  This has been especially true in the past two decades in the San Francisco Bay-Delta Estuary (Figure 7), commonly referred to as the period of the Pelagic Organism Decline.  It is an open question whether the American shad are simply experiencing the decline like the native fish, or contributing to the native declines, or both.

The likely answer is both.  All the fish suffer in drought.  All the fish do not recover completely after droughts.  All the fish populations exhibit a long-term downward population spiral.  For some, it is a spiral toward extinction.  Even in decline, some nonnatives like American shad and striped bass can have increasing effects on the natives facing extinction.  If that is the case, then we should do everything possible to at least provide habitat conditions that favor native fish over nonnative fish.  The fact is that, in many cases, nonnative fish, including shad and striped bass, are more resilient than the native fish.  That is because the physical habitat and water management increasingly are less favorable to the native species.  We need to reverse this trend.

For more recent discussion on Central Valley American shad see:

https://calwatercenter.org/american-shad-the-deltas-most-abundant-and-least-considered-anadromous-fish/

Figure 1. Wet year 2019 American shad juvenile catch-size distribution in Bay-Delta spring 20-mm Survey.

Figure 2. Wet year 2019 American shad juvenile catch-size distribution in Bay-Delta Summer Townet Survey.

Figure 2. Wet year 2019 American shad juvenile catch-size distribution in Bay-Delta Summer Townet Survey.

Figure 3. Wet year 2019 salvage and export rates of juvenile American shad at south Delta export facilities.

Figure 4. Wet year 2019 catch distribution of juvenile American shad in September Fall Midwater Trawl Survey.

Figure 5. Wet year 2019 American shad catch distribution versus salinity (EC) for September Fall Midwater Trawl Survey. Red line indicates shad concentrate in low-salinity zone (5-15k EC).

Figure 6. Wet year 2011 Delta smelt catch distribution versus salinity (EC) for September Fall Midwater Trawl Survey. Red line indicates smelt concentrate in low-salinity zone (5-15k EC).

Figure 7. Catch index of American shad juveniles in Fall Midwater Trawl Surveys 1967-2021. Recent drought periods noted.

A Ridiculous Premise

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A recent post from the Center for California Water Resources Policy and Management (Center) discusses the extinction of the Delta smelt.  The post starts by saying, “To be sure, the delta smelt’s numbers are in decline.”  That is a real understatement, but it contains some acknowledgement of the facts.

The author goes on to say, “It might fairly be argued that prime contributors to the delta smelt’s distressed status are California’s resource agencies.”  The ostensible rationale for this attribution is, first, that the resource agencies don’t look for smelt in the right places in the right way.  Second, because the agencies can’t find the smelt, “they have resisted managing the species ‘adaptively’” based on the monitoring that they don’t do.

This ridiculous premise suggests the decline has not been caused by excessive exports of water from the Bay-Delta watershed over the past five decades, but by the resource agencies who don’t know where to find and thus protect the smelt.

The author argues: “The agencies persist in mobilizing trawler-based open-water fish surveys, originally intended to census juvenile striped bass, as their primary means of monitoring delta smelt and the Delta’s other protected fish species.”  This statement is simply untrue.  To provide better coverage of “open-water” pelagic smelt, the Interagency Ecological Program (IEP) in recent decades added the Larval Survey, the 20-mm Survey, the Kodiak Trawl Survey, and most recently the Enhanced Delta Smelt Monitoring Program (EDSM).   All of these surveys, plus the historic Fall Midwater Trawl and Summer Townet Surveys (and 50 years of Delta Export Fish Salvage Surveys), show the smelt’s catastrophic decline and march toward extinction.

But the author insists that the smelt are out there somewhere.  “The surveys sample neither the relevant habitat strata used by those fishes nor the extent of their ‘closed’ populations, which would allow for estimates of the sizes of their populations.”  If the smelt are out there in “closed populations” whose numbers would change the conclusions about the smelt’s catastrophic downward trend, then surely the author and the water purveyors who have a vested interest in finding those populations can muster some evidence and show the agencies and the rest of the world where to look.

Basic review and analyses of the available information show the decline of Delta smelt is highly associated with increasing exports and associated factors (see my many posts on this subject).  The partial truth in the notion that the resource agencies have been complicit in the decline of Delta smelt stems from agency inaction to cut back those exports consistent with biological sustainability.  Agency managers don’t lack information and scientific method.  They lack the political courage to deploy them.