Geology topics

Paul Stumpner

Publications and source records attributed to Paul Stumpner.

14 recordsLinked to original sources

USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California↗

USGS2024

A machine learning tool for design of behavioral fish barriers in the Sacramento-San Joaquin River Delta

Executive Summary Survival of out-migrating juvenile salmonids ( Oncorhynchus spp.) through the Sacramento-San Joaquin River Delta averages less than 33 percent, depending on water flow through the delta, and is partially governed by the distribution of fish among three Sacramento River distributaries: Sutter, Steamboat, and Georgiana sloughs. Behavioral altering structures in the junctions of the distributaries can effectively increase entrainment into favorable routes, thereby increasing through-delta (Verona to Chips Island, California) survival. The effectiveness of these structures, hence forth called “behavioral barriers,” are dependent on shape, length, location, barrier type, and water velocity, which is governed by Sacramento River discharge (hereinafter referred to as “flow”). We developed a machine learning tool to optimize behavioral barrier designs at up to three junctions within the Sacramento-San Joaquin Delta for improving through-delta survival of juvenile winter-run Chinook salmon ( Oncorhynchus tshawytscha ). This barrier optimization tool (BOT) works by evolving barrier solutions in one to three junctions by repeatedly simulating survival of populations of Sacramento River origin fish as they pass through the Delta. Over approximately 6,000 simulations per junction, the BOT converges on barrier designs that result in the greatest average survival given simulated environmental conditions. Survival at each iteration of the model is simulated using a modified version of the salmon travel time and routing simulation (STARS) model. In the BOT, STARS is modified by replacing probabilistic route determinations with an individual based model (IBM) that simulates fish behavior to predict the entrainment rates in each junction. The IBM allows the flexibility to explore how entrainment changes with evolving barrier designs. We used juvenile winter-run-sized Chinook salmon catch data collected at Knights Landing from 1997 to 2011 to create realistic arrival and spatial distributions of simulated fish within the BOT that varied among water years (hereafter years). We demonstrated the capabilities of the BOT by comparing optimized barrier solutions and their resulting simulated improvement in survival among three scenarios that differed in the number of junctions with barriers (Georgiana Slough, Steamboat Slough, or both) and the barrier operational period (early: November 1–March 15, or late: January 1–April 30). In this initial demonstration of the BOT we only considered a bioacoustic fish fence (BAFF) at Georgiana Slough and a floating fish guidance structure (FFGS) at Steamboat Slough. The increase in simulated through-delta fish survival ranged from 1.0 to 6.3 percent among the optimized barrier designs. The most effective Georgiana Slough barrier design predicted improved survival by 6.3 percent and was chosen by the California Department of Water Resources (DWR) as the Georgiana Slough salmon migratory barrier planned for operation annually from 2023 to 2030 at Georgiana Slough in response to the 2020 California Department of Fish and Wildlife’s (CDFW) Incidental Take Permit Minimization Measure 8.9.1 (California Department of Fish and Wildlife [CDFW], 2020). When barriers were simulated in both junctions, the percentages of simulated winter-run Chinook salmon interacting with a barrier at Steamboat or Georgiana sloughs were 95 percent given the early operational period and 48 percent given the late operational period. When barriers were simulated at both sloughs, the optimal barrier at Steamboat Slough effectively routed fish into the Sacramento River. This is because the Georgiana Slough barrier reduced routing into Georgiana Slough where survival is low, which resulted in higher survival for fish routed down the Sacramento River at Steamboat Slough than fish routed down Steamboat Slough. Whereas when no barrier was simulated at Georgiana Slough, the optimized barrier at Steamboat Slough routed fish into Steamboat Slough. This is because survival was higher through Steamboat Slough than the Sacramento River and Georgiana Slough combined. The greatest improvement in survival (6.3 percent) was predicted over the earlier operational period with only a barrier at Georgiana Slough.

California↗

USGS2023

Hydrodynamics structure plankton communities and interactions in a freshwater tidal estuary

Drivers of phytoplankton and zooplankton dynamics vary spatially and temporally in estuaries due to variation in hydrodynamic exchange and residence time, complicating efforts to understand controls on food web productivity. We conducted approximately monthly (2012–2019; n = 74) longitudinal sampling at 10 fixed stations along a freshwater tidal terminal channel in the San Francisco Estuary, California, characterized by seaward to landward gradients in water residence time, turbidity, nutrient concentrations, and plankton community composition. We used multivariate autoregressive state space (MARSS) models to quantify environmental (abiotic) and biotic controls on phytoplankton and mesozooplankton biomass. The importance of specific abiotic drivers (e.g., water temperature, turbidity, nutrients) and trophic interactions differed significantly among hydrodynamic exchange zones with different mean residence times. Abiotic drivers explained more variation in phytoplankton and zooplankton dynamics than a model including only trophic interactions, but individual phytoplankton–zooplankton interactions explained more variation than individual abiotic drivers. Interactions between zooplankton and phytoplankton were strongest in landward reaches with the longest residence times and the highest zooplankton biomass. Interactions between cryptophytes and both copepods and cladocerans were stronger than interactions between bacillariophytes (diatoms) and zooplankton taxa, despite contributing less biovolume in all but the most landward reaches. Our results demonstrate that trophic interactions and their relative strengths vary in a hydrodynamic context, contributing to food web heterogeneity within estuaries at spatial scales smaller than the freshwater to marine transition.

California↗

USGS2023

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non-native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping.

California↗

USGS2022

Whole-ecosystem experiment illustrates short timescale hydrodynamic, light, and nutrient control of primary production in a terminal slough

Estuaries are among the most productive of aquatic ecosystems. Yet the collective understanding of patterns and drivers of primary production in estuaries is incomplete, in part due to complex hydrodynamics and multiple controlling factors that vary at a range of temporal and spatial scales. A whole-ecosystem experiment was conducted in a deep, pelagically dominated terminal channel of the Sacramento-San Joaquin Delta (California, USA) that seasonally appears to become nitrogen limited, to test whether adding calcium nitrate would stimulate primary productivity or increase phytoplankton density. Production did not respond consistently to fertilization, in part because nitrate and phytoplankton were dispersed away from the manipulated area within 1–3 days. Temporal and spatial patterns of gross primary production were more strongly related to stratification and light availability (i.e., turbidity) than nitrogen, highlighting the role of hydrodynamics in regulating system production. Similarly, chlorophyll was positively related not only to stratification but also to nitrogen—with a positive interaction—suggesting stratification may trigger nutrient limitation. The average rate of primary production (4.3 g O 2 m −2 d −1 ), metabolic N demand (0.023 mg N L −1 d −1 ), and ambient dissolved inorganic nitrogen concentration (0.03 mg N L −1 ) indicate that nitrogen can become limiting in time and space, especially during episodic stratification events when phytoplankton are isolated within the photic zone, or farther upstream where water clarity increases, dispersive flux decreases, and stratification is stronger and more frequent. The role of hydrodynamics in organizing habitat connectivity and regulating physical and chemical processes at multiple temporal and spatial scales is critical for determining resource availability and evaluating biogeochemical processes in estuaries.

California↗

USGS2021

Dispersion and stratification dynamics in the upper Sacramento River deep water ship channel

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosystems through their influence on primary production. The San Francisco Estuary (estuary) is a low-productivity ecosystem, which is in part responsible for constraining higher trophic levels, including fishes. Many research and habitat-restoration efforts trying to increase primary production have been conducted, including, as described here, a whole-ecosystem nutrient addition experiment where calcium nitrate was applied in the Sacramento River Deep Water Ship Channel (DWSC) to see if phytoplankton production could be increased and exported out of the DWSC. As an integral part of this experiment, we investigated the physical mechanisms that control mixing, and how these mechanisms affect the strength and duration of thermal stratification, which we revealed as critical for controlling phytoplankton dynamics in the relatively turbid upper DWSC. Analysis of a suite of mixing mechanisms and time-scales show that both tidal currents and wind control mixing rates and stratification dynamics in the DWSC. Longitudinal and vertical dispersion increased during periods of high wind, during which wind speed influenced dispersion more than tidal currents. Thermal stratification developed most days, which slowed vertical mixing but was rapidly broken down by wind-induced mixing. Stratification rarely persisted for longer than 24 hours, limiting phytoplankton production in the study area. The interaction between physical mechanisms that control mixing rates, mediate stratification dynamics, and ultimately limit primary production in the DWSC may be useful in informing habitat restoration elsewhere in the Delta and in other turbid aquatic environments.

California↗

USGS2021

Assessment of multiple ecosystem metabolism methods in an estuary

Ecosystem metabolism is a key ecological attribute and easy to describe, but quantifying metabolism in estuaries is challenging. Properly scaling measurements through time and space requires consideration of hydrodynamics and mixing water from heterogeneous sources, making any estimation uncertain. Here, we compared three methods for modeling ecosystem metabolism in a portion of the Sacramento-San Joaquin Delta. Metabolism estimates based on laboratory incubations, continuous in situ buoys, and an oxygen isotope approach all indicated the system was net heterotrophic, and calculated rates were comparable in magnitude when averaged over the 2-month study. Daily metabolic rates based on in situ buoys were the most variable, likely due to horizontal and vertical advection and poor portrayal of the dissolved oxygen budget. After temporally averaging in situ buoy estimates or smoothing the dissolved oxygen time series for tidal effects, rates were more comparable to the other methods, which may be necessary to account for tidal advection and unbalanced contributions from subhabitats within the metabolic footprint. Incubation-based rates represent the finest temporal and spatial scale and only account for pelagic processes, which may explain why incubation-based rates were lower than the other two methods. The oxygen isotope method provided temporally and spatially integrated rates that were bracketed by the other two methods and may be a valuable tool in systems matching the model requirements. Because uncertainty arises in each method from a number of assumptions and scaling calculations, the resolution of metabolic rates in estuaries is likely coarser and more variable than in other aquatic ecosystems.

California↗

USGS2020

Hydrodynamics drive pelagic communities and food web structure in a tidal environment

Hydrodynamic processes can lead to the accumulation and/or dispersal of water column constituents, including sediment, phytoplankton, and particulate detritus. Using a combination of field observations and stable isotope tracing tools, we identified how hydrodynamic processes influenced physical habitat, pelagic communities, and food web structure in a freshwater tidal system. The pelagic habitat of a terminal channel differed spatially, likely aligning with differences in hydrodynamics. Three zones that we classified by exchange with downstream habitat had distinct water quality characteristics, supported different densities of zooplankton and nekton, and exhibited disparate support from benthic and pelagic trophic pathways to pelagic consumers. Hydrodynamically driven zones and their emergent characteristics appeared sensitive to hydrology, as elevated runoff was correlated with a shift in hydrodynamic habitat and organismal distributions. The results of our study highlight the relationship between hydrodynamic processes, biological responses, and climate, and suggest that understanding the physical process can improve understanding of pelagic habitats and communities.

California↗

USGS2020

A lagrangian-to-eulerian metric to identify estuarine pelagic habitats

Estuaries are among the world’s most productive ecosystems, but recent natural and anthropogenic changes have stressed these ecosystems. Tools to assess estuarine pelagic habitats are important to support and maintain healthy ecosystem function. In this work, we demonstrate that estuarine pelagic habitats can be identified by a simple ratio, termed the LE ratio, that takes into account the tidal excursion along a channel (a Lagrangian length scale) and the distance along that channel (an Eulerian length scale). To develop and assess this concept, numerical simulations of the 1D advection–dispersion equation of a conservative tracer and tidal excursion estimates based on data were used to formulize a conceptual model and to define exchange zones within a tidal channel. This conceptual model was then used to predict the extent of pelagic habitats in a terminal channel network in the Sacramento–San Joaquin Delta. Exchange zones mapped onto these channels were found to be in good agreement with independent estimates of residence time. Sensitivity analyses of the numerical model suggest that productive pelagic habitats can be expanded by a factor of 2 by either increasing dispersion or increasing spring–neap variability in mean tidal velocity. Such changes can also enhance flushing in upper channel reaches. These findings are relevant for tidal marsh restoration projects that aim to expand beneficial aquatic habitats by varying exchange or residence time over the spring–neap cycle, because this variability may interact synergistically with varying rates of phytoplankton growth due to spatiotemporal changes in environmental conditions.

Estuaries and Coasts↗

USGS2020

Effects of tidally varying river flow on entrainment of juvenile salmon into Sutter and Steamboat Sloughs

Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management actions (e.g., fish guidance structures) to modify routing probabilities at this location. Main Content View Larger 1 Sponsored by the Delta Science Program and the UC Davis Muir Institute ABSTRACT Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access SFEWS Volume 19 | Issue 2 | Article 4 https://doi.org/10.15447/sfews.2021v19iss2art4 * Corresponding author: rperry@usgs.gov 1 Western Fisheries Research Center US Geological Survey Cook, WA 98605 USA 2 California Water Science Center US Geological Survey Sacramento, CA 95819 USA 3 Current address: Mid-Columbia Fish and Wildlife Conservation Office Yakima Basin Program US Fish and Wildlife Service Yakima, WA 98903 USA the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management RESEARCH Effects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Sloughs Jason G. Romine 1,3 , Russell W. Perry* 1 , Paul R. Stumpner 2 , Aaron R. Blake 2 , Jon R. Burau 2 2 VOLUME 19, ISSUE 2, ARTICLE 4 actions (e.g., fish guidance structures) to modify routing probabilities at this location. KEY WORDS Telemetry, juvenile salmon, migration routing, survival INTRODUCTION The Sacramento–San Joaquin River Delta (hereafter referred to as “the Delta”) is a complex series of channels and embayments in west central California of the United States. The Delta has undergone drastic transformation through construction of dikes, levees, reclaimed land, dredged canals and cuts, and water export projects (Nichols et al. 1986). The loss of habitat coupled with introduction of non-native piscivorous fishes has led to the decline of several salmonid stocks that utilize the Delta (Lindley 2009; National Marine Fisheries Service 2014). The physical complexity of the Delta poses significant challenges for understanding how juvenile salmon negotiate the complex channel network and survive in different migration routes. Yet such information is critical for understanding how water-management actions, such as operation of water diversions, influence survival of juvenile salmon. Through-Delta survival of juvenile Chinook Salmon that emigrate from the Sacramento River ranges from 10% to 80%, depending on river flow and migration route (Perry et al. 2018). The Delta can be broken down into four primary routes: (1) Sacramento River, (2) Steamboat and Sutter sloughs, (3) Georgiana Slough, and (4) Delta Cross Channel (DCC). Fish that remain in the Sacramento River consistently have the highest survival (Perry et al. 2010, 2013, 2018). However, fish that enter the interior Delta—the region to the south of the Sacramento River (Figure 1)—have the lowest survival among all routes and survive at less than half the rate of fish in the Sacramento River, likely as a result of longer migration times and exposure to non-native predators (Newman and Brandes 2010; Perry et al. 2018). On average, fish that migrate through Steamboat and Sutter sloughs exhibit survival similar to fish that remain in the Sacramento River at high flows but have lower survival at low flows (Perry et al. 2018). Because of differences in survival among migration routes, the proportion of fish that use each route affects the total survival of the population. Therefore, understanding the drivers behind fish routing in the Delta is imperative to inform management actions that help in the recovery of imperiled salmonid populations in the Central Valley. For example, Perry et al. (2013) found that total survival through the Delta could be increased by up to 7 percentage points by eliminating entrainment into Georgiana Slough and the DCC. These findings led to investigation of management actions to reduce entrainment into the DCC (Plumb et al. 2016) and Georgiana Slough (Perry et al. 2014). Both physical and non-physical barriers have been tested at the entrance to Georgiana Slough divergence (Perry et al. 2014; Romine et al. 2016). A non-physical barrier was able to reduce entrainment to the interior Delta through Georgiana Slough (Perry et al. 2014), but a floating fish-guidance structure reduced entrainment to a lesser extent (Romine et al. 2016). Research and engineering solutions to minimize entrainment have focused on the Georgiana Slough divergence, the DCC divergence, and the Old River divergence in the San Joaquin River (Buchanan et al. 2013; SJRG 2013). However, there has been little focus on understanding fish routing dynamics at other primary river junctions in the Delta, such as Sutter and Steamboat sloughs. Sutter and Steamboat sloughs diverge from the Sacramento about 10 km upstream from the DCC and Georgiana slough, and represent the first major junction that juvenile salmon encounter as they enter the Delta from the Sacramento River ( Figure 1 ). Because Sutter and Steamboat sloughs are upstream of the entrance to the interior Delta via the DCC and Georgiana Slough (Figure 1), juvenile salmon that enter Sutter and Steamboat sloughs avoid entrainment into the interior Delta where survival is low. Thus, management actions to increase entrainment could increase overall.

Sacramento–San Joaquin Delta↗

USGS2020

Combining models of the critical streakline and the cross-sectional distribution of juvenile salmon to predict fish routing at river junctions

Because fish that enter the interior Delta have poorer survival than those emigrating via the Sacramento River, understanding the mechanisms that drive entrainment rates at side channel junctions is critically important for the management of imperiled juvenile salmon. Here, we implement a previously proposed process-based conceptual model to study entrainment rates based on three linked elements: the entrainment zone, critical streakline, and cross-sectional distribution of fish. The critical streakline is the location along a channel cross-section immediately upstream of a junction that forms the spatial divide between parcels of water that enter a side channel or remain in the main channel. The critical streakline therefore divides the main channel into entrainment zones within which fish would likely enter each channel. Combined with information about the cross-sectional distribution of fish upstream of a junction, this conceptual model provides a means to predict fish entrainment into each channel. To apply this conceptual model, we combined statistical models of the critical streakline, the cross-sectional distribution of acoustic tagged juvenile Chinook salmon, and their probability of entrainment into Georgiana Slough. We fit joint beta regression and logistic regression models to acoustic telemetry data gathered in 2011 and 2012 to estimate the cross-sectional distribution of fish upstream of the junction, and to estimate the probability of entrainment for fish on either side of the critical streakline. We show that entrainment rates can be predicted by understanding how the combination of critical streakline position and cross-sectional distribution of fish co-vary as a function of environmental covariates. By integrating over individual positions and entrainment fates to arrive at population-level entrain probability in relation to environmental covariates, our model offers managers a simple but powerful tool to evaluate how alternative actions affect migrating fish.

California↗

USGS2017

A simulation method for combining hydrodynamic data and acoustic tag tracks to predict the entrainment of juvenile salmonids onto the Yolo Bypass under future engineering scenarios

During water year 2016 the U.S. Geological Survey California Water Science Center (USGS) collaborated with the California Department of Water Resources (DWR) to conduct a joint hydrodynamic and fisheries study to acquire data that could be used to evaluate the effects of proposed modifications to the Fremont Weir on outmigrating juvenile Chinook salmon. During this study the USGS surgically implanted acoustic tags in juvenile late fall run Chinook salmon from the Coleman National Fish Hatchery, released the acoustically tagged juvenile salmon into the Sacramento River upstream of the Fremont Weir, and tracked their movements as they emigrated past the western end of the Fremont Weir. The USGS analyzed tracking data from the acoustically tagged juvenile salmon along with detailed hydrodynamic data collected in the Sacramento River during the winter/spring of water year 2016 in the vicinity of the western end of the Fremont Weir to assess the potential for enhancing the entrainment of Sacramento River Chinook salmon onto the Yolo Bypass under six different Fremont Weir modification scenarios. Each modification scenario consists of a notch or multiple notches in the Fremont Weir which are designed to divert a portion of the Sacramento River onto the Yolo Bypass when the Sacramento River is below the crest of the Fremont Weir. The primary goal of this entrainment analysis was to investigate how the location of the notch or notches in each scenario affected the entrainment of juvenile Chinook salmon onto the Yolo Bypass, and to predict the notch location or locations that would result in maximum entrainment under each modification scenario. Stumpner et al.’s (in review) analysis of hydraulic data collected during the 2016 study period showed that backwater effects in the Sacramento River created significant variability in the relationship between Sacramento River stage and the proportion of the Sacramento River flow that we expect to be diverted onto the Yolo Bypass under the modification scenarios. Because of this variability, accurately evaluating the entrainment potential of possible notch locations for each scenario required combining historic abundance data for juvenile Sacramento River Chinook salmon with historic hydraulic data for the Sacramento River in the vicinity of the Fremont Weir, so that the entrainment estimates would reflect the covariance between Sacramento River stage, Sacramento River discharge, and juvenile salmon abundance within the historic record. We used a Monte Carlo simulation framework to combine the high resolution hydrodynamic data and acoustic tag track data collected in 2016 with historic juvenile salmon abundance, Sacramento River stage, and Sacramento River discharge data from a period spanning water years 1996-2010 to assess the entrainment potential of different weir modification scenarios under historic conditions. The scenarios we simulated consisted of four single notch configurations, and two multiple notch configurations in the vicinity of the western end of the Fremont Weir. For each notch configuration the 15-water-year entrainment simulation was repeated for 63 possible notch locations in the vicinity of the western end of the Fremont Weir. This approach allowed us to assess the effect of notch location on the entrainment of juvenile salmonids onto the Yolo Bypass for each of the six notch configurations that we evaluated. The entrainment simulations showed that the location of each notch configuration had a major impact on the entrainment for each scenario; the predicted entrainment of some scenarios varied by as much as 400% based on where the notch (or notches) was (were) located in the study area. All of the single notch scenarios performed best when they were located within a 330 ft (100 meter) long section of the Sacramento River bank adjacent to the western terminus of the Fremont Weir (Table 1). Both of the multiple notch scenarios performed best when their upstream notches were located about 660 ft (200 meters) upstream of the western terminus of the Fremont Weir (Table 1). The results of the entrainment simulations indicated that for each notch configuration the same notch location produced near-maximum entrainment regardless of run abundance timing; this result suggests that there are areas within the study are where a notch (or notches) can be sited to achieve maximum entrainment for all runs (barring significant behavioral or physiological differences between runs). In addition, the simulation results indicate that for each notch configuration the same location is expected to produce nearmaximum entrainment for both wet water years and dry water years. Based on the results of the entrainment simulation we make three general recommendations for strategies to improve the entrainment potential of a notch in the Fremont Weir: 1) Comparisons between the maximum entrainment potential for each scenario suggested that total entrainment of winter run, spring run, and fall run salmon onto the Yolo Bypass can be increased by increasing the amount of water entering a notch when the Sacramento River stage is between 19 ft and 22 ft NAVD88; this could be accomplished by lowering notch invert elevations or by adding a control section to the Sacramento River to raise stage for a given discharge. 2) The relationship between Sacramento River stage and entrainment for each scenario indicated that entrainment efficiency for each scenario declined significantly once Sacramento River stage exceeded bankfull (approximately 28.5 ft NAVD88). This effect was likely due to inundation of the floodplain between the Sacramento River and the Fremont Weir; Stumpner et. al (In Review) have documented a reduction in the strength of the secondary circulation and centralization of the downwelling zone in the Sacramento River when this floodplain is inundated. Therefore, increasing the height of the river right bank of the Sacramento River to coincide with the height of the Fremont Weir is recommended to increase entrainment at higher stages. 3) Bathymetric features upstream of notch openings appeared to have a major impact on the entrainment potential of the simulated notches. For this reason we recommend taking care to avoid siting notches immediately downstream of bank features that alter the sidewall boundary layer, and we expect that smoothing the bank bathymetry upstream of a notch will enhance entrainment. Finally, we caution that the entrainment simulation was based on the behavior of large hatchery smolts, so it is likely that our results will be sensitive to any differences in behavior and physiology between these hatchery surrogates and naturally migrating juvenile salmon.

California↗

USGS2016

Evaluation of a floating fish guidance structure at a hydrodynamically complex river junction in the Sacramento-San Joaquin River Delta, California, USA

Survival of out-migrating juvenile Chinook salmon ( Oncorhynchus tshawytscha ) in the Sacramento–San Joaquin River delta, California, USA, varies by migration route. Survival of salmonids that enter the interior and southern Delta can be as low as half that of salmonids that remain in the main-stem Sacramento River. Reducing entrainment into the higher-mortality routes, such as Georgiana Slough, should increase overall survival. In spring 2014, a floating fish-guidance structure (FFGS) designed to reduce entrainment into Georgiana Slough was deployed just upstream of the Georgiana Slough divergence. We used acoustic telemetry to evaluate the effect of the FFGS on Chinook entrainment to Georgiana Slough. At intermediate discharge (200–400 m 3 s –1 ), entrainment into Georgiana Slough was five percentage points lower when the FFGS was in the on state (19.1% on; 23.9% off). At higher discharge (>400 m 3 s –1 ), entrainment was higher when the FFGS was in the on state (19.3% on; 9.7% off), and at lower discharge (0–200 m 3 s –1 ) entrainment was lower when the FFGS was in the on state (43.7% on; 47.3% off). We found that discharge, cross-stream fish position, time of day, and proportion of flow remaining in the Sacramento River contributed to the probability of being entrained to Georgiana Slough.

California↗

USGS2008

Dual-RiverSonde measurements of two-dimensional river flow patterns

Two-dimensional river flow patterns have been measured using a pair of RiverSondes in two experiments in the Sacramento-San Joaquin River Delta system of central California during April and October 2007. An experiment was conducted at Walnut Grove, California in order to explore the use of dual RiverSondes to measure flow patterns at a location which is important in the study of juvenile fish migration. The data available during the first experiment were limited by low wind, so a second experiment was conducted at Threemile Slough where wind conditions and surface turbulence historically have resulted in abundant data. Both experiments included ADCP near-surface velocity measurements from either manned or unmanned boats. Both experiments showed good comparisons between the RiverSonde and ADCP measurements. The flow conditions at both locations are dominated by tidal effects, with partial flow reversal at Walnut Grove and complete flow reversal at Threemile Slough. Both systems showed complex flow patterns during the flow reversals. Quantitative comparisons between the RiverSondes and an ADCP on a manned boat at Walnut Grove showed mean differences of 4.5 cm/s in the u (eastward) and 7.6 cm/s in the v (northward) components, and RMS differences of 14.7 cm/s in the u component and 21.0 cm/s in the v component. Quantitative comparisons between the RiverSondes and ADCPs on autonomous survey vessels at Threemile Slough showed mean differences of 0.007 cm/s in the u component and 0.5 cm/s in the v component, and RMS differences of 7.9 cm/s in the u component and 13.5 cm/s in the v component after obvious outliers were removed. ?? 2008 IEEE.

Conference Paper↗