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The Delta Ecological Flows Tool: record of design (v1.1)
Abstract
The Ecological Flows Tool (EFT) is a decision support system that demonstrates how changes in flow management (and other actions) result in changes to the physical habitats for multiple species within the Sacramento River and the San Francisco Delta. This document provides the as-built Record of Design for
the focal species and habitat indicators developed for version 1 of the Delta Ecological Flows Tool
(DeltaEFT) branch of EFT. The Record of Design for the Sacramento Ecological Flows Tool (SacEFT)
version 2 branch of EFT is documented separately (see: ESSA 2011a). Between 2004 and 2008 The
Nature Conservancy (TNC) conducted the Sacramento River Ecological Flows Study in which TNC and
its project partners developed a decision analysis tool that incorporates physical models of the Sacramento
River with biophysical habitat models for six Sacramento River species. The resultant tool, SacEFT, links
flow management actions to focal species outcomes on the mainstem Sacramento River (see ESSA 2011a
for details). Building on the success of SacEFT, this software architecture was extended starting in 2008
to include a range of Delta specific ecological indicators and management actions through construction of
version 1 of the DeltaEFT branch of the software. Version 1 of DeltaEFT, the subject of this document,
was completed in September 2012. Importantly, completion of DeltaEFT now provides the ability to
explicitly link upstream (Sacramento River) ecological responses evaluated with SacEFT to ecosystem
responses in the Delta evaluated with DeltaEFT. "SacEFT" and "DeltaEFT" are collectively referred to as
"EFT".
EFT works by integrating a range of representative functional ecological response indicators with key
physical variables obtained from widely used hydrologic models (e.g., CalSim, DSM2, USRDOM). EFT
more transparently relates multiple attributes of the flow regime to multiple species’ life history needs,
contributing to an effective understanding of flow and non-flow (gravel augmentation, rip-rap removal,
levee set-back) restoration actions on multiple focal species and their habitats. The hallmark of the EFT
approach is integration and clear communication of ecological trade-offs associated with different water
operation alternatives. This capability has been illustrated in recent applications of EFT to EIS/R
investigations for North of Delta Off-stream Storage (NODOS; TNC and ESSA 2011) and the Bay Delta
Conservation Plan (BDCP; ESSA 2011b and see BDCP Plan documents1).
EFT is structured as an ‘ecological plug-in’ to existing physical models that are commonly used for water
planning in the Central Valley. Rather than reinventing models, EFT utilizes output data sets from daily
disaggregations of CalSim, DSM2 and other models that are used to investigate water delivery and other
standards set for the CVP and SWP water system. EFT utilizes these data and adds ecological calculations
(algorithms) to evaluate effects of water re-operation and conveyance and storage project changes on
multiple ecosystem targets.
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Computer model results are becoming more prominent in water policy deliberations in California. CalSim II is the most prominent water management model in California, and has become central to a variety of water management and policy issues and controversies. This paper reports on the results of an extensive set of loosely-structured interviews with members of California’s technical and policy-oriented water management community regarding the use and development of CalSim II in California. The interviewers reflect on the thoughts of interviewees and how such interview activities can further policy-effective modeling and technical activities for water management. CalSim II is a complex model of a complex part of California’s changing multi-purpose water system. As such, analytical controversies and misunderstandings are inevitable. Ideally, a model and its associated data would perform an additional service as a forum to resolve technical controversies and continually improve quantitative understanding of the system. While CalSim II is generally seen as a significant improvement over previous models, a wide variety of ideas are suggested for improvements.
The delta smelt (Hypomesus transpacificus) is a small and relatively obscure fish that has recently risen to become a major focus of environmental concern in California. It was formally abundant in the low-salinity and freshwater habitats of the northeastern San Francisco Estuary, but is now listed as threatened under the Federal and California State Endangered Species Acts. In the decade following the listings scientific understanding has increased substantially, yet several key aspects of its biology and ecological relationships within the highly urbanized estuary remain uncertain. A key area of controversy centers on impacts to delta smelt associated with exporting large volumes of freshwater from the estuary to supply California’s significant agricultural and urban water demands. The lack of appropriate data, however, impedes efforts to resolve these issues and develop sound management and restoration alternatives. Delta smelt has an unusual life history strategy relative to many fishes. Some aspects of its biology are similar to other coastal fishes, particularly salmonids. Smelts in the genus, Hypomesus, occur throughout the Pacific Rim, have variable life history strategies, and are able to adapt rapidly to local environments. By comparison, delta smelt has a tiny geographic range being confined to a thin margin of low salinity habitat in the estuary. It primarily lives only a year, has relatively low fecundity, and pelagic larvae; life history attributes that are unusual when compared with many fishes worldwide. A small proportion of delta smelt lives two years. These individuals are relatively highly fecund but are so few in number that their reproductive contribution only may be of benefit to the population after years of extremely poor spawning success and survival. Provisioning of reproductive effort by these older fish may reflect a bet-hedging tactic to insure population persistence. Overall, the population persists by maximizing growth, survival, and reproductive success on an annual basis despite an array of limiting factors that can occur at specific times and locations. Variability in spawning success and larval survival is induced by climate and other environmental and anthropogenic factors that operate between winter and mid-summer. However, spawning microhabitats with egg deposition have not been discovered. Spawning success appears to be timed to lunar periods within a water temperature range of about 15 to 20°C. Longer spawning seasons in cooler years can produce more cohorts and on average higher numbers of adult delta smelt. Cohorts spaced in time have different probabilities of encountering various sources of mortality, including entrainment in freshwater export operations, pulses of toxic pesticides, food shortages and predation by exotic species. Density dependence may provide an upper limit on the numbers of juvenile delta smelt surviving to the adult stage. This may occur during late summer in years when juvenile abundance is high relative to habitat carrying capacity. Factors defining the carrying capacity for juvenile delta smelt are unknown, but may include a shrinking volume of physically suitable habitat combined with a high density of competing planktivorous fishes during late summer and fall. Understanding the relative importance of anthropogenic effects on the population can be improved through better estimates of abundance and measurements of potentially limiting processes. There is little information on losses of larval delta smelt (less than 20 mm fork length, FL) to the export facilities. Use of a population model suggests that water export operations can impact the abundance of post-larval (about 20 mm FL) delta smelt, but these effects may not reflect on adult abundance due to other processes operating in the intervening period. Effects from changes to the estuarine food web by exotic species and toxic chemicals occur but measuring their influence on population abundance is difficult. Although delta smelt recently performed well enough to meet the current restoration criteria, analyses presented here suggest that there is still a high probability that the population will decline in the near future; the most recent abundance index (2004) is the lowest on record. Overall, the limited distribution, short life span and low reproductive capacity, as well as relatively strict physical and feeding requirements, are indications that delta smelt is at risk to catastrophe in a fluctuating environment. Unfortunately, options for avoiding potential declines through management and restoration are currently limited by large gaps in knowledge. Monitoring of spring water temperatures, however, may provide a useful tool for determining when to reduce entrainment in water export facilities. Actions that target carrying capacity may ultimately provide the most benefit, but it is not clear how that can be achieved given the current state of knowledge, and the limited tools available for restoration. Overall, a better understanding of the life history, habitat requirements, and limiting factors will be essential for developing tools for management and restoration. Therefore, given the implications for managing California water supply and the current state of population abundance, a good investment would be to fill the critical data gaps outlined here through a comprehensive program of research.
This monograph presents an extensive review of the biology and management of Chinook salmon and steelhead in the Central Valley of California. Relevant data and publications on these populations are summarized and discussed in the context of the wider professional literature, with emphasis on the importance of evolutionary considerations in the assessment of populations and in their management, the need to manage populations together with their environments, and the contradiction between maintaining a major hatchery program to support a mixed-stock ocean fishery and trying to maintain or restore populations adapted to natural or semi-natural habitats. Recommendations are presented for management and monitoring—for example for a thorough review of hatchery operations, for more emphasis on monitoring individual-based factors such the physiological condition and growth rates of juveniles, and for simulation of major restoration actions and monitoring programs. The 17 chapters cover major conceptsin salmon biology and conceptual foundations for management, and Central Valley Chinook and steelhead populations and their habitat, growth and migration, habitat use, harvest, hatcheries, modeling, monitoring, and management.
AbSTRACT The biological productivity of river-dominated estuaries is affected strongly by variation in freshwater inflow, which affects nursery habitat quality. Previous research has shown this is generally true in the upper San Francisco Estuary, California, USA; however, one endemic species of high management importance, delta smelt (Hypomesus transpacificus), has shown ambiguous population responses to river inflow variation. We hypothesized that population-level associations with abiotic habitat metrics have not been apparent because the effects occur seasonally , and at spatial scales smaller than the entire upper San Francisco Estuary. We tested this hypothesis by applying regression techniques and principal components analysis (PCA) to a long-term data-set (1970–2004) of summertime fish catch, and concurrently measured water quality (specific conductance, Secchi disk depth, and water temperature). We found that all three water quality variables predicted delta smelt occurrence, and we identified three distinct geographic regions that had similar long-term trends in delta smelt capture probabilities. The primary habitat region was centered on the confluence of the Sacramento and San Joaquin rivers; delta smelt relative abundance was typically highest in the Confluence region throughout the study period. There were two marginal habitat regions—including one centered on Suisun Bay—where specific conductance was highest and delta smelt relative abundance varied with specific conductance. The second marginal habitat region was centered on the San Joaquin River and southern Sacramento-San Joaquin Delta. The San Joaquin region had the warmest water temperatures and the highest water clarity, which increased strongly in this region during 1970–2004. In the San Joaquin region, where delta smelt relative abundance was correlated with water clarity, catches declined rapidly to zero from 1970–1978 and remained consistently near zero thereafter. However, when we combined these regional results into estuary-wide means, there were no significant relationships between any of the water quality variables and delta smelt relative abundance. Our findings support the hypothesis that basic water quality parameters are predictors of delta smelt relative abundance, but only at regional spatial scales. san Francisco estuary & watershed science 2
Striped bass, Morone saxatilis, and largemouth bass, Micropterus salmoides, are two of the top piscivores in California's San Francisco Estuary. The relative abundance of age-0 striped bass has plummeted since the late 1960s, whereas the abundance of largemouth bass has increased since the early 1990s. Major changes to the estuarine food web have made it a likely place for significant striped bass food limita-tion, and despite their population increase, there is evidence that young largemouth bass might also be chronically food-limited. Food limita-tion can be thought of as a context-dependent stressor, meaning that population-level consequences of food limitation are discernable only when they are severe enough to override other factors influencing the growth and mortality of young fishes. The purpose of this study was to clarify the role that food limitation plays in the early life history of striped bass and largemouth bass. I used a combination of previously published beach seine data and bioenergetic modeling (BEM) to evaluate the ques-tion, which species is likely more food-limited during its first growing season? I hypothesized that age-0 striped bass would show evidence of greater food limitation than largemouth bass (as indexed by realized vs. potential growth). The BEM simulations predicted that largemouth bass would grow larger than striped bass given the water temperature histories these fish experienced in the Sacramento-San Joaquin Delta during summer-autumn 2001 and 2003. However, the striped bass col-lected during autumn were larger than the largemouth bass and had thus performed better relative to BEM predictions. I conclude that age-0 striped bass were less food limited than age-0 largemouth bass in these recent years. As discussed, the upsurge of largemouth bass is likely the outcome of low survival in an expanding area of suitable habitat, whereas striped bass food limitation covaries in time with high entrainment loss and declining abiotic habitat suitability. This contrast provides a counter-intuitive example of the context-dependence of food limitation in these sympatric fish populations.
Splittail Pogonichthys macrolepidotus, an endemic cyprinid of the Sacramento–San Joaquin estuary, has been proposed for listing as threatened under the U.S. Endangered Species Act. Almost continuous low outflow conditions in the estuary from 1987 to 1994 led to reduced abundance of young splittails, but adult abundance did not decline consistently except in the downstream portion of the species' range. This range had decreased primarily as a result of historical levee and dam construction but did not appear to have changed substantially in the past 20 years. The distribution of young splittails appears to be relatively plastic on an interannual basis. Evidence of the resilience of the species was seen when high freshwater outflows in extremely wet years (such as 1982, 1983, 1986, and 1995) resulted in high numbers of young splittails. Splittail year-class strength was positively related to freshwater outflow during the spawning season. High outflow inundates the floodplain, which provides spawning, rearing, and foraging habitat. The relatively long life span, high reproductive capacity, and broad environmental tolerances of splittails are contrasted with delta smelt Hypomesus transpacificus and longfin smelt Spirinchus thaleichthys, other native species of special concern in the system.
