Category Archives: Bay-Delta

Review of Decade-Old Misdirection on Delta Smelt

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For several decades, scientific literature and state and federal permits have documented the decline in Delta smelt and promoted actions designed to slow the Delta smelt’s demise or even reverse it. However, that soundly based and widely promoted recovery strategy has often been undermined by some scientists and engineers funded by water-related industries and users intent on minimizing constraints on their water operations. The undermining of traditional science and regulatory institutions has been insidious and aggressive, to the point of nearly destroying the Central Valley and Bay-Delta ecosystem and many of its public trust resources. I know this from working nearly 50 years on these conflicts.

A recent interest takes me back to some of these undermining efforts from a decade ago. In this post, I evaluate past theories from such efforts and further characterize the “science” used to support them. I believe such hindsight reviews of these historical efforts helps to daylight and counteract similar present and future attempts to undermine institutional protections. I focus on unsubstantiated conclusions, on misuse of data or analytical tools, and on the authors’ general strategy of promoting misinformation to argue their points.

The “scientific paper” I review in this post on Delta smelt is William J. Miller, Bryan F. J. Manly, Dennis D. Murphy, David Fullerton & Rob Roy Ramey (Miller et al.) (2012): An Investigation of Factors Affecting the Decline of Delta Smelt (Hypomesus transpacificus) in the Sacramento-San Joaquin Estuary, Reviews in Fisheries Science, 20:1, 1-19, DOI: 10.1080/10641262.2011.634930.1

In commenting below, I show quotations from the paper in quotes and italics.

Comments on the Authors’ Major Conclusion in the Abstract

  • “Strong evidence was found of density-dependent population regulation.” The authors made no attempt to describe such “regulation” of the Delta smelt population. First, the meaning of “strong” is unclear. I assume the authors mean that two variables appear closely related. I found a “density-dependent” relationship (see my Figure 1, below), wherein summer abundance is positively related to previous fall abundance. Second, the meaning of “regulation” is unclear. I assume by “regulation” they mean that at very high numbers of adults, recruitment tails off, as implied in the blue curve in Figure 1. But as shown in the figure, the inference is far from a “strong evidence” of “population regulation” due to density.


  • “The density of prey was the most important environmental factor explaining variations in delta smelt abundance from 1972 to 2006 and over the recent period of decline in the abundance of the fish.” Association does not necessarily mean cause and effect. In Figure 1, I show that wet years have, on average, ten times more recruitment than dry years. That could be why prey appears important, because smelt prey densities (and feeding habitat conditions) tend to be better in wet years. However, water temperatures are also higher in dry years, as is entrainment of smelt in the south Delta. Just because prey has the highest correlation does not mean it is the cause or has any direct effect. These variables are not independent from one another.


  • “Predation and water temperature showed possible effects.” The authors also noted other positive relationships. The problem with such statistical analyses is that the “independent variables” being tested against smelt abundance are not independent from each other. Therefore, no judgement can be made as to cause and relationship, only inferences.


  • “Entrainment of delta smelt at south Delta pumping plants showed statistically significant effects on adult-to-juvenile survival but not over the fish’s life cycle.” Here again, cause and effect are inferred. The authors state the fact that recruitment is related to the number of adult spawners, yet they immediately state otherwise. Entrainment of adult smelt is something that has been measured – as salvage at the south Delta pumping plants. It is a variable that can readily be compared to the fall trawl index. But entrainment of larvae and early juveniles (6-25 mm young) is not measured, and thus this part of the “fish’s life cycle” cannot be statistically related to any smelt index.


  • “Neither the volume of water with suitable abiotic attributes nor other factors with indirect effects, including the location of the 2 ppt isohaline in the Delta in the previous fall (“fall X2”), explained delta smelt population trends beyond those accounted for by prey density.” When a variable shows minimal relationship, it cannot be concluded that it has no effect, or compared in strength to another “independent” variable (another potential factor). Fall X2 may only be important in some years, and thus its effect relationship may be non-linear.2 The relationships being studied may also change with time (as indicated in Figure 1). Relationships are also often complicated by factors that act in complex ways. Posts on my own reviews generally support the Fall X2 action for a variety of reasons.3 Thus, the authors’ conclusion or implication that Fall X2 is not important is not reasonable. The prey factor simply takes up more of the variability in the multi-factor statistical analysis, and thus masks the role of Fall X2.

Comments on the Introduction

  • “The need for immediate conservation responses is acute, but that need confronts another unfortunate delta smelt reality—perhaps less is known about the habitat of delta smelt, resources essential to its persistence, and the environmental stressors causing its low population numbers than is known about any other listed species.” This statement has no basis and is simply untrue. Delta smelt are one of the most studied fish on Earth.


  • “The life cycle of the tiny estuarine fish takes place in turbid, open waters, making it impossible to observe its behavior and account for many of its vital ecological relationships.” Over the past five decades, there have been numerous studies and volumes of monitoring data on Delta smelt “ecological relationships”. One only has to look at Figure 1. As for behavior, Delta smelt have been raised and observed in labs and hatcheries for over two decades. Two decades ago, I could literally smell them and their prime habitat. I could also tell where they would be by measuring salinity and water temperature.


  • “Several candidate factors have plausible mechanisms of effect on delta smelt numbers, but previous attempts to relate environmental stressors to the decline of this fish were not able to identify the factors responsible for the recent declines in the abundance index to near-extinction levels.” The evidence from the 1987-1992 drought (see Figure 1 for one of many examples) was quite compelling, enough to get the species listed under the Endangered Species Act, first as threatened (1993), then as endangered (2010). All the “plausible factors” could be related to drought conditions that had become worse with ever-increasing effects of water management (increasing exports year after year). Protections instituted in the aftermath of the drought and listing4 included designation of critical habitat (1994) and a recovery plan (1996), as well as multiple federal biological opinions and habitat conservation plans, and state incidental take permits over the next two decades. Recovery programs, including the Central Valley Project Improvement Program (CVPIA) and CALFED Bay-Delta Ecosystem Restoration Program (ERP), focused on Delta smelt recovery. Those efforts led directly to significant progress in 2010-2011; however, weakened protections during the 2012-2015 drought ended the potential for further progress.


  • “No field data have been derived from experimnts that directly relate delta smelt population responses to variation in physical and biotic conditions.” This statement is a gross untruth. The data that support Figure 1 are “field data.” Many of the various monitoring surveys (e.g., Larval Survey, 20-mm survey, Townet Survey) yield indices that show such relationships.

Comments on the Discussion

I could go on in the same -vein through the paper’s introduction, methods, results, and discussion, but I will skip to the paper’s primary conclusions as presented in the discussion section.

  • [E]ntrainment was not a statistically significant factor in survival from fall to fall”. First, entrainment of early smelt life stages into the federal and state south-Delta export facilities is not monitored. Second, monitoring that does help assess entrainment risk shows the inherent risk (Figures 2 and 3). Third, the fall midwater trawl survey includes the fall period of high adult salvage losses that contributed to the population decline, a data feature that compromises the fall-to-fall survival-factor analysis.


  • “Changes in prey density appear to best explain the sharp drop in delta smelt abundance in this century”. First, Delta-smelt prey density is also directly and indirectly related to south Delta exports. Second, an annual index of smelt prey is a very crude way to analyze the effects of prey through the various life stages of smelt or its annual abundance indices.


  • “Density dependence was an important factor affecting survival from fall to summer, summer to fall, and fall to fall.” First, there is little or no evidence that high densities reduce recruitment or survival, at least in the period of record. Historically, available habitat had to limit the population size and recruitment near their highest abundance levels. Second, there is also no evidence that very low population levels lead to higher survival, growth, or abundance (from less crowding and competition). These are the two features that generally contribute to density-dependent population regulation. What the authors term density-dependence is simply the fact that more adults lead to more young, and more young lead to more adults. Water management and use lead to fewer adults and young – density independent population regulation controls population abundance.


  • “This finding indicates that density dependence must be accounted for in analyses directed at identifying factors that are important to the abundance of delta smelt.” This only means that any factors that lead to fewer adults or young damages the population, and that those losses are compounded across life stages. There are no remaining compensatory density-dependent capacity reserves in the population to absorb or counter such added mortality.


  • “There was some indication that average water temperature and calanoid copepod biomass (a general measure of prey density) in April–June were important contributors to survival of delta smelt from fall to summer.” Again, these are factors affected by water management. Delta exports pull warm water and invertebrates into the south Delta. These are density-independent factors.


  • “Furthermore, predation in April–June, representing the combined effects of water clarity and abundance of the predators, inland silversides, largemouth bass, crappie, and sunfish, was important to delta smelt survival from fall to fall.” Again, the effects of predation are increased by the warmer, clearer water pulled into the interior Delta by south Delta exports.


  • “Furthermore, in the case of delta smelt, not only does an effects hierarchy suggest the use of simple linear regression models, but the low sampling errors in abundance relative to process errors indicates that this simple and transparent method of analysis is an appropriate method for identifying environmental factors with direct effects. Therefore, at least for delta smelt and perhaps for other fish for which sampling errors in abundance are relatively low, simple linear regression, as an alternative to more complex life-cycle models, can produce informative results.” Such analyses have been inappropriately used to confuse interpretations of long-term environmental and fish population dynamics data, and to misinform and misdirect environmental resource management and regulatory processes, institutional and public awareness, and the public’s confidence in these societal and cultural institutions.

Summary and Conclusions

Miller et al. (2012), the “scientific” paper referenced in this post, is an example of efforts on the part of state and federal water contractors to point the blame for resource declines on factors other than water operations that overuse and abuse public trust resources. It is important not only in itself, but also because it combines with similar efforts to become part of a body of alternative “science” that is cited by water suppliers and managers in repetition of the narrative that water operations have minimal effect on the Delta smelt’s decline.

I recognize that such efforts may appear in “peer reviewed” journals, and can be sincere efforts to contribute to the understanding of the science underlying resource management. I am simply registering the need for caution and consideration of the source and the content of all analytical and interpretive efforts related to information used by those responsible for protecting our public trust resources.

Figure 1. Delta smelt spawner-recruit relationship. Figure generated by Tom Cannon.

Figure 2. Delta smelt survey catch pattern from mid-June 2012, one of the last surveys with an abundance of larval smelt produced from the strong 2011 brood spawning population. The red lines show the approximate location of the upstream location of X2 (low salinity zone).

Figure 3. Typical dry year spring-summer tidally-filtered (net) or daily-average hydrology for the Delta, showing net flow rates toward south Delta export pumps.

The Delta in April-June 2022 under TUCP

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A lot has been said about the drought’s effect on water supplies for cities and farms, but little is said about how Delta fish are faring.  Freshwater inflow to the Delta was about half of normal in April through June 2022 because of the State Water Board Order approving the Department of Water Resources (DWR) and the Bureau of Reclamation’s Temporary Urgency Change Petition  (TUCP) for Delta operations.  With some of this limited Delta inflow going to water users during April, May and June, little was going to the fish.

The State Water Board granted the TUCP because Central Valley reservoir storage was so low at the end of winter in this third year of drought.  During drought, most of the Delta’s late spring and summer inflow comes from releases from storage in Shasta, Oroville, and Folsom reservoirs.

The TUCP has ended, and the normal operating rules for the Delta under Water Rights Decision 1641 have gone back into effect as of July 1.  It is now a good moment to review the effects of this most recent TUCP.

Conditions Under TUCP (April-June 2022)

Delta inflow from the Sacramento River and tributaries averaged about 7500 cfs while the TUCP was in effect (Figure 1).  Releases from Folsom Reservoir averaged 1000-2000 cfs of this inflow.  Releases from Oroville Reservoir varied widely, but averaged about 2500 cfs over the period.  Other inflow came from the Sacramento River (Shasta Reservoir) and its tributaries, which during the TUCP period averaged about 3000-4000 cfs.  The San Joaquin River and its tributaries contributed on average another 1000 cfs to Delta inflow.

There are three main uses of Delta inflow when inflow is low: repelling salt water, south Delta exports, and in-Delta use.  South Delta exports were about 1300 cfs while the TUCP was in effect.  Delta outflow, holding back the salt water, required roughly 4000 or more depending on tides.  Net in-delta use (water diversions other than south Delta exports) accounted for the rest.

Salinity (EC, mS/cm) at Emmaton (west Delta Figure 2) , normally kept near 500 per the state standard for agriculture, increased to levels ranging from 500 to 8000 (Figure 2), with daily average of 2000 to 4000, four to eight times the standard.

At Jersey Point, where the standard is 450-750 EC, salinity ranged from 1200 to 2300 in June (Figure 3).

Conditions After TUCP (Early July 2022)

After the TUCP expired, conditions changed as regulatory requirements returned requirements under Decision 1641.  Delta inflow increased to 12,500 cfs (Figure 1).  At this date, salinity has fallen toward the appropriate salinity standards (Figures 3 and 4).

What does this mean for the Delta and its Fish? 

  1. The agricultural salinity standard of 500 mmhos at Emmaton near Sherman Island in the Sacramento River channel was “relaxed” under the TUCP (Figure 3). Salt water was able to push further upstream and mix to a further extent with inflow.  The daily salinity (EC) range of approximately 500-8500 mmhos, an increased level of spring salinity not seen since the 2014 and 2015 drought under earlier TUCPs.
  2. Likewise, the average daily salinity (EC) standard at Jersey Point near Sherman Island in the San Joaquin River channel (Figure 4) was also not being met.
  3. Salinity was managed under the TUCP to meet the minimum drinking water standards (<800 mmhos) near municipal water supply diversions in the central Delta (Figure 5). (I would not drink this water or put it on plants.)
  4. Throughout June, net flows in the Old and Middle River channels in the central Delta were southward toward the South Delta export pumps (Figures 2 and 6).
  5. While the TUCP was in effect, salt water moved upstream in the Sacramento River channel near Rio Vista and into Cache Slough (Figure 7). Within the Cache Slough Complex, water moved upstream (Figure 8) in part due to water diversions in the north Delta.
  6. Delta inflows from the Sacramento River at Freeport fell below 10,000 cfs from April through June 2022 as allowed under the TUCP (Figure 1). This drop led to the increases in salinity noted in Figures 2-8.
  7. Low Delta inflows also contributed to higher water temperatures throughout the Delta during and after the TUCP period (Figures 9 and 10). Water temperatures above 72 degrees are detrimental to most of the native Delta fish.

Conclusions:

  • The TUCP allowed reduced Delta inflows that preserved some reservoir storage in critical drought year 2022.
  • Inflows dropped below the normal 10,000-12,000 range that keep Delta salinity at Emmaton and Jersey Pt below the 500 mmhos agricultural salinity standard.
  • Central and north Delta water diversions from the Delta’s pool of freshwater contributed to upstream movement and loss in quality and quantity of the low-salinity zone, a critical nursery habitat of Delta native fishes.
  • The shift in the location of these important habitats into the north and central Delta, and the associated warming from the more-eastward position and lower net flows represent a serious impact on Delta native fishes including Delta smelt, longfin smelt, green and white sturgeon, winter-run, fall-run, and spring-run salmon, and steelhead, which use these habitats through the spring and summer for rearing and migration.

Figure 1. Delta inflow (cfs) from the Sacramento River as measured at Freeport in 2022. Note the TUCP allows streamflow at Freeport to be reduced below the 10,000-12,000 cfs range that is normally necessary to meet Delta salinity standards at Emmaton and Jersey Pt.

Figure 2. West Delta salinity gage locations with net flow direction during TUCP period April-June 2022.

Figure 3. Salinity (EC) range at Emmaton in west Delta in 2022.

Figure 4. Salinity (EC) at Jersey Point in west Delta in 2022.

Figure 5. Salinity (EC) in the central Delta in Old River channel in 2022.

Figure 6. Net flows in central Delta Old River and Middle River channels in 2022.

Figure 7. Salinity (EC) in Cache Slough channel of north Delta near Rio Vista in 2022.

Figure 8. Net flows in Cache Slough near Liberty Island in 2022.

Figure 9. Water temperature of the Sacramento River near Freeport in 2022.

Figure 10. Water temperatures in the Delta and Delta inflows May-July 2022.

EMM – Emmaton on the Sacramento River channel in west Delta.

WLK – Lower Sacramento River below Wilkins Slough above the mouth of the Feather River.

PPT – Prisoners Pt in the central Delta channel of the San Joaquin River.

DLC – Sacramento River channel in the north Delta at the Delta Cross Channel.

OBI – Old River in central Delta.

RVB – Rio Vista Bridge in west Delta channel of the Sacramento River.

SJJ – San Joaquin channel in west Delta at Jersey Pt.

OH4 – Old River in central Delta.

ANH – San Joaquin River channel of west Delta at Antioch.

MSD – San Joaquin River channel at entrance to Delta at Mossdale.

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.