Delta Smelt: Life History and Decline of a Once-Abundant Species in the San Francisco Estuary

University of California, Davis (UC Davis) | July 1st, 2016

The delta smelt is endemic to the upper San Francisco Estuary. Much of its historic habitat is no longer available and remaining habitat is increasingly unable to sustain

The delta smelt is endemic to the upper San Francisco Estuary. Much of its historic habitat is no longer available and remaining habitat is increasingly unable to sustain the population. As a listed species living in the central node of California’s water supply system, delta smelt has been the focus of a large research effort to understand causes of decline and identify ways to recover the species. Since 2008, a remarkable record of innovative research on delta smelt has been achieved, which is summarized here. Unfortunately, research has not prevented the smelt’s continued decline, which is the result of multiple, interacting factors. A major driver of decline is change to the Delta ecosystem from water exports, resulting in reduced outflows and high levels of entrainment in the large pumps of the South Delta. Invasions of alien species, encouraged by environmental change, have also played a contributing role in the decline. Severe drought effects have pushed delta smelt to record low levels in 2014–2015 and diverse and substantial management actions are needed to preserve delta smelt.

Designing Monitoring Programs in an Adaptive Management Context for Regional Multiple Species Conservation Plans

U.S. Geological Survey (USGS) | January 1st, 2004

Increasing numbers of regional, multiple species conservation plans have been developed in California since the early 1990s. However, building effective monitoring and ad

Increasing numbers of regional, multiple species conservation plans have been developed in California since the early 1990s. However, building effective monitoring and adaptive management programs to support these plans has remained a challenge. In addition to collecting data on the status of resources and the results of management actions, monitoring programs for these plans need to resolve critical uncertainties and channel information into effective decisionmaking.  Because of the broad goals of many regional conservation plans, monitoring programs need to address ecosystem integrity and biodiversity while also tracking species “covered” by plan permits. In this document we provide a step-by-step procedure for developing effective monitoring programs in an adaptive management context. The guidance provided here has been gleaned from experience with large multiple species plans in southern California. The process begins with clearly defining program objectives, partitioning the program into manageable but meaningful pieces, and developing management-oriented conceptual models of system function. Then, based on the objectives and conceptual models, monitoring recommendations and critical uncertainties can be identified and a coordinated program designed. We include practical examples and insights from programs in southern California and discuss the evolution of monitoring and adaptive management programs through three successive stages: 1) inventorying resources and identifying relationships; 2) pilot testing of long-term monitoring and resolving critical management uncertainties; and 3) implementing long-term monitoring and adaptive management. Ultimately, the success of regional conservation planning depends on the ability of monitoring programs to confront the challenges of adaptively managing and monitoring complex ecosystems and diverse arrays of sensitive species.

Draft finding of no significant impact, 2-Gates Fish Protection Demonstration Project.

U.S. Bureau of Reclamation (USBR) | November 13th, 2009

The proposed Demonstration Project is a 5-year experiment to validate a new delta smelt behavioral model and study the effects of modifying flows in the Sacramento-San Jo

The proposed Demonstration Project is a 5-year experiment to validate a new delta smelt behavioral model and study the effects of modifying flows in the Sacramento-San Joaquin Delta (Delta) to protect delta smelt and other sensitive aquatic species from entrainment in Central Valley Project (CVP) and State Water Project (SWP) export pumps. Research suggests that the pre-spawning migration of adult delta smelt is tied to sediment/suspended particles in the water (turbidity). Temporary gates would be placed across Old River and Connection Slough in the central Delta and operated from December to March to keep turbid water away from the CVP and SWP export pumps, thus keeping adult delta smelt away from the pumps, and in March and June to prevent larvae and juvenile delta smelt from being entrained by the export pumps.

DRERIP Ecosystem Conceptual Model: Chinook Salmon & Steelhead

California Department of Fish and Wildlife (CDFW) | September 4th, 2012

This report constitutes the conceptual model for Chinook and steelhead for the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The report describes

This report constitutes the conceptual model for Chinook and steelhead for the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The report describes conceptual models, not numerical models, but several important considerations apply to both kinds, especially when they are used for management of living natural resources. First, the proper purpose of models is to help people think, not to think for them. Ignoring this can be disastrous, as exemplified by the current economic crisis. The world of credit default swaps was built on highly sophisticated models that persuaded many intelligent people that the associated risk was negligible, but they failed to recognize that a market based on houses that people could not pay for from their earnings is unsustainable. In short, the most important output of a good conceptual or numerical model is clear thinking. To help people think, the model must be focused on selected features of the world that are thought to be important for the purpose at hand: in this case, management of the Delta. A model that tries to include everything will be too complex to be useful for this purpose. Second, to be useful for management of natural living resources, numerical models must be unrealistic, because our knowledge of such resources is incomplete, and is based on data that includes measurement errors. According to Ludwig‘s paradox, "Effective management models cannot be realistic" (Ludwig 1994:516), because two kinds of uncertainty must be balanced (Figure I-1; see Ch. 14 in Williams (2006) for elaboration of this point). In our view, something similar applies to conceptual models of natural systems: to be useful, they must be simple. A schematic of the wiring in some electronic device is a conceptual model that may be useful as well as complex, but trying to develop a similar schematic of an ecosystem or part of an ecosystem is not useful, because our knowledge of such a system is much less complete than our knowledge of engineered devices, and we have only estimates of the relevant parameters. Finally, reality is too complex to capture with a single model. Eric Lander, a noted geneticist who co-chairs President Obama‘s Council of Advisors on Science and Technology, recently remarked that "You can never capture something like an economy, a genome or an ecosystem with one model or one taxonomy – it all depends on the questions you want to ask." (NY Times, 11/11/08). Models are tools that we use to try to think, and multi-purpose tools generally do nothing well. Therefore, although the complete life cycle of Chinook and steelhead is described here, the parts or aspects of the cycle that we think may be affected by management of the Delta are emphasized, and we try to keep it as simple as possible. More detail on most of the topics described here can be found in Quinn (2005), or in Williams (2006), from which this document draws very heavily.

DRERIP Ecosystem Conceptual Model: Floodplain

California Department of Fish and Wildlife (CDFW) | January 22nd, 2008

Elements common to all models (Figure 1). Gray shapes (“plaques” in Word parlance) are other DRERIP models. Brown polygons are modifying factors. Pink rectangles are

Elements common to all models (Figure 1). Gray shapes (“plaques” in Word parlance) are other DRERIP models. Brown polygons are modifying factors. Pink rectangles are primary outputs of direct interest to Delta restoration planners (e.g., splittail). Blue rectangles are hydrological characteristics or variables, primarily pertaining to the primary river that is the source of inundation to the floodplain of interest but some rectangles represent “secondary hydrology” such as water deriving from direction precipitation on the floodplain, and groundwater and tributary inputs. Blue-green rectangles represent inundated habitat characteristics – properties of the floodplain during periods of inundation. Model 1 (Creating the Template) captures the linkages and processes that create the habitat mosaic—the physical template of a given floodplain, such as topography and vegetative communities (Figure 2). Note that habitat mosaic is more than vegetative communities as it also includes topographic features like side channels, oxbows, and wetlands. This is a very basic model, so we didn’t attempt to use the information-coded arrows to indicate importance, predictability, etc. This model describes how floodplain topography and vegetation, important features treated as more or less static in the other models, are created and maintained. This model encompasses time scales ranging from a single flood event (e.g., bank erosion) to decades or centuries (successional processes in a floodplain forest). Delta restoration planners can use model 1 to understand management options for creating and maintaining habitat mosaics on a given floodplain. Model 2 (Inundating the template) depicts how a given floodplain, with topography and vegetation created within Model 1, is inundated by river flows and other sources of water to create specific conditions within the inundated floodplain that are important to the species or processes described in model set 3 (Figure 3). The hydrology first encounters river-floodplain topography (e.g., the relative elevations of floodplain to river stage) to determine if the floodplain becomes inundated; the other linkages only occur if flow magnitude is capable of exceeding the inundation threshold. Inundation is a function of flow magnitude in the river, along with contributions from other hydrological sources (e.g., local tributaries, high water table), and the relative elevation and connectivity of the river-floodplain topography. If inundation occurs, the floodwaters interact with the topography and vegetation created in Model 1. As inundation occurs across this mosaic it results in a variety of inundated habitat characteristics—conditions that directly affect biota and processes during the period of inundation. These inundated habitat characteristics are the primary inputs for Model Set 3. This model is primarily focused at the temporal scale of a single flood season. Delta restoration planners can use model 2 to evaluate how management actions can influence the inundation of floodplain habitat mosaics and characteristics of the inundated habitat. Model Set 3 (Management outputs) illustrates how the inundated habitat characteristics, developed in Model 2, interact with a few other key elements to influence the production of biota of direct interest to delta restoration planners, including algae, zooplankton, splittail, and juvenile Chinook salmon (Figures 4 - 7). Model Set 3 encompasses a temporal scale of a single flood season. Model Set 3 can be used to evaluate how specific characteristics of the inundated floodplain affect specific outputs of management interest. Figure 4 provides a basic overview of the inputs and outputs and relationships between the models in Model Set 3. Figure 5 focuses on the production of algae (phytoplankton and epibenthic algae) and zooplankton, structured as a food web. Figures 6 and 7 show how the inundated habitat characteristics and base of the food web (algae and zooplankton) affect the production of splittail and Chinook salmon, respectively. Primary management outputs from floodplain models: 1. Primary productivity, in terms of phytoplankton, the most nutritious organic matter for the downstream delta (Muller-Solger et al. 2002) and secondary productivity (zooplankton and macroinvertebrates). Because several important species in the delta are food-limited, as indicated by low first-year survival, floodplain restoration has been promoted as a means of increasing productivity to these species and ecosystems (Jassby and Cloern 2000). 2. Juvenile Chinook 3. Splittail 4. Habitat mosaic and riparian structure for a variety of species. The first three management outputs are Model 3 outputs. For these a user can work backwards through the models to understand how management options can increase the productivity of a specific desired output. For example, if the desired output is biologically available Carbon for downstream ecosystems (algae), then Figure 5 (Model 3) indicates that residence time and intra-annual frequency are important characteristics; for these characteristics of inundation to occur, Figure 3 (Model 2) indicates that the frequency of inundation can be influenced either through hydrologic or topographic manipulations, and the narrative for Model 1 provides background information on the processes that create and maintain floodplain topography. The management output ‘riparian structure’ is a Model 1 output.

DRERIP Ecosystem Conceptual Model: Green sturgeon

California Department of Fish and Wildlife (CDFW) | December 27th, 2008

The purpose of this report is to develop a conceptual life history model of North American green sturgeon (Acipenser medirostris) and the factors that affect reproduction

The purpose of this report is to develop a conceptual life history model of North American green sturgeon (Acipenser medirostris) and the factors that affect reproduction, growth, and survival in the Sacramento and San Joaquin rivers and San Francisco Bay-Delta. This model can be used to organize, visualize, and evaluate how the complex life history of green sturgeon relates to the spatial and temporal variability of riverine and estuarine ecosystems and potential consequences of ecosystem restoration and water management alternatives. This model is compatible with the suite of environmental and species models developed by the Department of Fish and Game Ecosystem Restoration Program (ERP) to assess and prioritize proposed restoration actions for the Delta. The model has a geographic emphasis on the Sacramento River and Bay-Delta regions, though the entire distribution of green sturgeon must be considered when population level responses are of concern, due to the unique, highly-migratory life history of this species. The conceptual life history model incorporates information from numerous sources about green sturgeon, often relying upon life history information from populations outside the Southern Distinct Population Segment (DPS) and occasionally considering information from the sympatric white sturgeon (A. transmontanus). While surrogate information from other North American sturgeon could have been used in the model, the distinctive anadromous and ecological characteristics of green sturgeon limited the utility of these species’ information. Due to the limits of quantitative information about green sturgeon, this model is presented in a qualitative narrative with numerical information provided, when available. While it will not provide quantitative limits on species take relative to maintaining a stable population size, it could be further developed into a population forecasting model since it divides the life history into life history stages, transition probabilities, and factors whose affects on reproduction and survival could be quantified. Life history stage transitions are visualized in a series of life stage submodels highlighting the processes and relationships among ecological factors influencing the transition between stages (Figures 1 and 2). A complex set of conditions and processes are necessary to determine whether an individual fish completes the transition from one life stage to the next. Our knowledge of green sturgeon life history remains limited as to the relative importance of biotic and abiotic factors critical for maintaining self-sustaining populations of green sturgeon. Thus, the importance, predictability, and understanding of each of these linkages are identified in the model. Lastly, a similar characterization of independent stressors is undertaken to describe potential factors affecting survival during each life history stage in a known geographic region. This model is dynamic and not intended to be a final version. As new information becomes available, the model should be refined so managers and biologists have the most current information available.

DRERIP Ecosystem Conceptual Model: Longfin smelt

California Department of Fish and Wildlife (CDFW) | May 1st, 2010

This model describes the importance of stressors on the life history of longfin smelt in the San Francisco Estuary. In addition, the model identifies the degree to which

This model describes the importance of stressors on the life history of longfin smelt in the San Francisco Estuary. In addition, the model identifies the degree to which we understand the nature of a relationship between stressors and successful completion of the life cycle (“understanding”) and the certainty surrounding how important a particular stressor is for a particular life stage (“certainty of impact”).

DRERIP Ecosystem Conceptual Model: White sturgeon

California Department of Fish and Wildlife (CDFW) | April 25th, 2011

The purpose of this report is to develop a conceptual life history model of white sturgeon (Acipenser transmontanus) and the factors that affect reproduction, growth, and

The purpose of this report is to develop a conceptual life history model of white sturgeon (Acipenser transmontanus) and the factors that affect reproduction, growth, and survival in the Sacramento-San Joaquin Rivers and San Francisco bay-delta. This model can be used to organize, visualize, and evaluate how the complex life history of white sturgeon relates to the spatial and temporal variability of riverine and estuarine ecosystems and potential consequences of ecosystem restoration and water management alternatives. This model is compatible with the suite of environmental and species models developed by the Department of Fish and Game Ecosystem Restoration Program (ERP) to assess and prioritize proposed restoration actions for the delta. The model has a geographic emphasis on the Sacramento River and bay-delta regions, though the entire distribution of white sturgeon should be considered when population level responses are of concern, due to the migratory life history of this species. The conceptual life history model incorporates information from numerous sources about white sturgeon, often relying upon life history information from populations outside California. While additional surrogate information from other North American sturgeons could have been used in the model, the distinctive diadromous and ecological characteristics of California white sturgeon limited the utility of these species’ information, thus information from other diadromous sturgeon species is only occasionally considered. Due to the limits of quantitative information about white sturgeon, this model is presented in a qualitative narrative, though numerical information is provided when available. While it will not provide quantitative limits on species take relative to maintaining a stable population size, it could be further developed into a population forecasting model since it divides the life history into life history stages, transition probabilities, and factors whose effects on reproduction and survival could be quantified. Life history stage transitions are visualized in a series of life stage submodels highlighting the processes and relationships among ecological factors influencing the transition between stages (Figures 1 and 2). A complex set of conditions and processes are necessary to determine whether an individual white sturgeon completes the transition from one life stage to the next. Our knowledge of how biotic and abiotic factors are critical for maintaining healthy populations is fairly basic. Thus, the importance, predictability, and understanding of each of these linkages are identified in the model. Lastly, a similar characterization of independent stressors is undertaken to describe potential factors affecting survival during each life history stage in a known geographic region. This model is dynamic and not intended to be a final version. As new data become available, the model should be refined so managers and biologists have the most current information available.

Effect of the South Delta Agricultural Barriers on Emigrating Juvenile Salmonids

California Department of Water Resources (DWR) | November 15th, 2018

The California Department of Water Resources’ (DWR) Temporary Barriers Project (TBP) is an ongoing project that installs, operates, and monitors up to four temporary ro

The California Department of Water Resources’ (DWR) Temporary Barriers Project (TBP) is an ongoing project that installs, operates, and monitors up to four temporary rock-fill barriers constructed in waterways located in the southern portion of the Sacramento-San Joaquin Delta (Delta) near the cities of Tracy and Lathrop in San Joaquin County, California (Figure 1-1). Three of the temporary barriers—Old River at Tracy (ORTB), Middle River (MRB), and Grant Line Canal (GLCB), collectively, the south Delta agricultural barriers (SDABs)—are constructed and operated during the agricultural irrigation season, usually April through November. The SDABs are designed to act as flow control structures, retaining tidal fresh water behind each barrier following a flood tide. The fourth barrier, Head of Old River Barrier (HORB), is installed during the spring and fall as a fish guidance barrier. The HORB is normally installed in the spring to prevent juvenile fall-run San Joaquin River Chinook Salmon (Oncorhynchus tshawytscha) and juvenile Central Valley steelhead (Oncorhynchus mykiss) 2 from emigrating through Old River toward the south Delta water export facilities at the intakes of the State Water Project (SWP) and federal Central Valley Project (CVP). In the fall, the HORB helps to guide adult San Joaquin River Chinook Salmon to spawning locations in the upper watershed. Installation, operation, and removal of the SDABs has the potential to harm, harass, or cause mortality to fish species of management concern to the National Marine Fisheries Service (NMFS), specifically, juvenile fall-run Chinook Salmon which are NMFS Species of Concern (NMFS 2010), juvenile Central Valley steelhead which is a threatened species, an Endangered Species Act (ESA) Section 10j experimental population (63 Federal Register [FR] 13347), and juvenile Green Sturgeon (Acipenser medirostris), also a federally listed threatened species (71 FR 17757). The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009).

Effects Analysis for the Delta Smelt Fall Habitat Action in 2019

U.S. Bureau of Reclamation (USBR) | August 1st, 2019