Monthly Archives: September 2022

Review of Decade-Old Misdirection on Delta Smelt

Posted on by

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.

Update on Shasta River – Summer 2022

Posted on by

In a post in July 2021, I discussed the problems facing Shasta River salmon.  An 8/20/22 article in CalMatters described how the problems became acute this summer when the local ranchers’ water association ignored the State’s emergency order to stop diverting water from the Shasta River in this drought year.  After complying for most of the summer, the ranchers diverted about 20 cfs of water for about a week in mid-August (Figure 1; blue line)

Figure 1. Streamflow in the lower Shasta River upstream of Montague. Ranchers complied with the State’s emergency drought order until mid August. After a week under the threat of fines they stopped diverting.

What the ranchers did in mid-August was simply what they had been doing for decades but were asked to stop in 2022 (see Figure 1, median for 37 years; orange line).

It appears based on the downstream Yreka gage that other ranchers also took part in ignoring the State’s mandate (Figure 2) as the deficit reached about 30 cfs.  These other diverters also returned to compliance with the mandate after a week of non-compliance.

Several reductions in Shasta River flow are not mentioned in the CalMatters article. The total water supply to the Shasta River from springs  originating from Mt. Shasta is somewhere between 250 and 300 cfs in most summers (Figure 3 shows summer of wet year 2017).  In critical drought year 2022, the total supply is closer to 200 cfs, because there are less spring inputs and demands are greater.  In general, about 40-50 cfs is taken out by large wells from the 100 cfs input of Big Springs (leaving the roughly 50 cfs of river flow reaching Montague in Figure 1).  The springs shown in Figure 3 provided less inflow in drought year 2022 than they did in 2017, because Lake Shastina is critically low and input from the upper river and its springs are lower (Figure 4).  The upper Shasta River also loses water at Weed to the city supply and to water bottlers.

Coho salmon once thrived in the Shasta River below Big Springs and in the upper Shasta River.  Coho have suffered for many decades under the historical pattern shown in Figures 1-3.  Some of the remnant population may have been living in the 20 miles of river below Montague this summer, until they were subjected to the low flows and very stressful water temperatures that came with the one week of unauthorized diversions.  There is also this year’s run of fall-run Chinook salmon holding in the Klamath River at the mouth of the Shasta River, awaiting sufficient flow and adequate water temperatures to migrate up the Shasta River.

The fact is that the State Water Board can’t solve a century-old problem with an emergency decree in one dry summer.  The State needs to develop a comprehensive solution for the Shasta River that provides 50 cfs of water for salmon year-round (at Montague Figure 1, and Yreka, Figure 2), out of the available 200-300 cfs supply.  Users need to share the rest equitably, especially in a drought year like 2022.

Figure 2. Streamflow in the lower Shasta River downstream of Yreka in the summer of 2022. Also shown is daily average mean flow for the previous 85 years.

Figure 3. Selected Shasta River hydrology in late May of wet year 2017. Roughly 150 cfs of the 300 cfs total basin inflow in this wet year is being diverted for agriculture, city water supply, and water bottling (Weed) with remainder reaches the Klamath River. Red numbers are larger diversions. The “X’s” denote major springs. Big Springs alone provides near 100 cfs. Of the roughly 100 cfs entering Lake Shastina (Dwinnell Reservoir) from Parks Creek and the upper Shasta River and its tributaries, only 16 cfs is released to the lower river below the dam. The remainder is stored and released to east-side irrigation canal (about 50 cfs). Red numbers and arrows indicate larger agricultural diversions. Up to 15 cfs is diverted to the upper Shasta River from the north fork of the Sacramento River, west of Mount Shasta. Blue dots show locations of river flow gages.

Figure 4. Hourly flow in the upper Shasta River in summer 2022 at Edgewood just downstream of the City of Weed.