This study evaluates the potential water availability in Barka Slough and the effects of changing hydrological conditions on the aquatic habitat of five protected species. Barka Slough is a historically perennial wetland at the downstream western end of the San Antonio Creek Valley watershed (SACVW). A previously published hydrologic model of the SACVW for 1948–2018 was extended to include 2019–2021 and then modified to simulate the future years of 2022–2051. Two models simulating the future years of 2022–2051 were constructed, each with different climate inputs: (1) a repeated historical climate and (2) a 2070-centered Drier Extreme Warming climate (2070 DEW). The model with the 2070 DEW climate had warmer temperatures and an increase in average annual precipitation driven by larger, albeit more infrequent, precipitation events than the model with the historical climate. Simulated groundwater pumpage resulted in cumulative groundwater storage depletion and groundwater-level decline in Barka Slough in both future models. The simulations indicate that Barka Slough may transition from a perennial to an ephemeral wetland. Streamflow, stream disconnection, and depth to groundwater are key habitat metrics for federally listed species in Barka Slough. Future seasonal conditions for each metric are more likely to affect federally listed species’ habitats under 2070 DEW climatic conditions. Future seasonal streamflow volume may negatively impact unarmored threespine stickleback (Gasterosteus aculeatus williamsoni) and tidewater goby (Eucyclogobis newberryi) habitats. Future seasonal stream disconnection may negatively impact the unarmored threespine stickleback habitat. Future groundwater-level decline may negatively impact Gambel’s watercress (Nasturtium gambelii) and La Graciosa thistle (Cirsium scariosum var. loncholepis) habitats and could influence the ability to use Barka Slough as a restoration or reintroduction site for these species. Results from this study can be used to inform water management decisions to sustain future groundwater availability in the SACVW.

Objective Stable isotopes are commonly used to understand the role of fishes in aquatic food webs. However, variability in species- and tissue-specific isotopic values can affect the inference that is drawn from a stable isotope study. We evaluated differences in stable isotopes of carbon (delta 13C) and nitrogen (delta 15N) among three tissue types (white muscle, caudal fin rays, and eye lenses) for Santa Ana Sucker Pantosteus santaanae and Arroyo Chub Gila orcuttii to inform the design of a stable isotope study in the Santa Ana River, an urban river that is located in southern California.Methods We used multivariate analyses to test for differences in the stable isotopes of carbon (delta 13C) and nitrogen (delta 15N) among the three tissue types that were collected from Santa Ana Sucker and Arroyo Chub. We also summarized the variability in isotopic values that was recorded over time in fish eye lenses and interpreted this variability in reference to the spatial patterns in isotopic values that have been previously reported throughout the Santa Ana River.Results We found that fin ray tissue and white muscle tissue were not significantly different for either isotope or fish species. Fish eye lenses were significantly higher in delta 13C than muscle tissue, and eye lenses were significantly higher in delta 15N than fin ray tissue for both fishes. We also found a greater range in delta 13C and delta 15N across eye lens layers for Santa Ana Sucker (delta 13C = 2.01 +/- 0.96 parts per thousand, delta 15N = 4.93 +/- 4.18 parts per thousand) than for Arroyo Chub (delta 13C = 0.96 +/- 0.65 parts per thousand, delta 15N = 4.63 +/- 1.45 parts per thousand).Conclusion Our results indicate that fin rays may be a viable nonlethal alternative to white muscle tissue for use in a stable isotope study of native fish of the Santa Ana River. Additionally, eye lenses could provide a chemical history of fishes within the river, but species-specific correction factors may be needed if stable isotope values for eye lenses are to be compared with more conventional tissue types (e.g., white muscle). Fin rays, white muscle, and eye lenses of Santa Ana Sucker and Arroyo Chub could be used with stable isotope tools to describe the diets and habitat use of these fishes over space and time in the Santa Ana River.

ObjectiveThe Redeye Bass Micropterus coosae is a piscivore introduced into California, which has become a threat to the state's endemic freshwater fishes. It has eliminated native fishes from the middle reaches of the Cosumnes River, our study stream, which is the largest stream without a major dam on its main stem in the Sacramento-San Joaquin River drainage, central California, USA. We thoroughly documented its novel life history and ecology in California to shed light on why it has been such a successful invader despite its relatively small native range.MethodsOver 4000 stable carbon and nitrogen isotope samples were utilized to refine our understanding of fish trophic position within the river food web, along with a stable isotope mixing model that accounts for uncertainty in trophic enrichment data.ResultGrowth was slow, with an adult size range of 9-25 cm standard length (SL), although few were larger than 15-cm SL (5-6 years old). Stable isotope analyses showed that Redeye Bass dominate the river ecosystem to the exclusion of most native fishes, occupying multiple trophic levels and microhabitats. Adults largely consumed non-native crayfish and large aquatic insects, while juveniles consumed aquatic insects, the size of prey increasing with Redeye Bass length. There was no evidence of cannibalism. Redeye Bass have effectively occupied the diverse trophic positions of at least four native fish species and have altered the trophic position of Rainbow Trout Oncorhynchus mykiss in sites where they co-occur with bass.ConclusionThe introduction of Redeye Bass poses a continuing threat to native stream fishes in California and elsewhere. The Redeye Bass is a predatory fish that is endemic to the Coosa River system, spanning Georgia and Alabama, in the southeastern United States, but introduced into California. It now dominates a California river ecosystem, eliminating native fishes and simplifying the food web. Its success demonstrates the unintended consequences of introducing even fish with a small native range into a region with an already stressed native fish fauna.

Effective restoration of tidal wetlands for fish communities requires clear goals and mechanistic understanding of the ecosystem drivers which affect fish distribution and abundance. We examined fish community responses to abiotic habitat features in two adjacent but dissimilar freshwater tidal wetlands in the Sacramento-San Joaquin Delta, CA, USA, each of which represents a potential restoration configuration. The first wetland was characterized by a broad, intertidal basin with relatively high hydrodynamic exchange with surrounding waterways. The second wetland was characterized by a dendritic network of shallow subtidal channels with relatively low hydrodynamic exchange. Fish community composition significantly differed between the two wetlands, based on permutational analysis of variance. Fish abundance within and among the two wetlands was also highly affected by specific geomorphic and hydrodynamic characteristics: distance from connection with the main external waterway, bed elevation, and water surface elevation. The physical configuration of a restored tidal wetland, in conjunction with the way tides move across the restored landscape, has strong implications for local fishes. Manipulating these elements to create a landscape mosaic of habitat configurations can be an effective tool for targeting desired restoration outcomes, such as specific fish communities or target fish densities.

First posted January 16, 2024 For additional information, contact: Director,California Water Science CenterU.S. Geological Survey6000 J Street, Placer HallSacramento, California 95819 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.

An understanding of oceanographic conditions and processes important to marine animal ecology is fundamental to the development of effective management and conservation actions. Longfin Smelt (Spirinchus thaleichthys) is a pelagic forage fish found in coastal and estuarine waters along the Pacific coast of North America from Alaska to central California. Substantial population declines in California’s San Francisco Estuary, where Longfin Smelt are protected under California’s Endangered Species Act, have prompted extensive study of estuarine factors associated with the decline. However, coastal factors that affect up to two-thirds of the Longfin Smelt life cycle are poorly understood and may be important drivers of population dynamics. We compiled coastal observations from numerous sources to estimate the range-wide coastal marine distribution of Longfin Smelt and assess habitat factors affecting distribution in the northeast Pacific Ocean. Based on maximum entropy species distribution models, Longfin Smelt distribution was correlated with depth, distance from the nearest estuary, sea surface temperature, and sea surface chlorophyll. Longfin Smelt were found in shallow, higher productivity coastal waters closer to estuaries, with depth and temperature the most consistent factors influencing distribution. Habitat suitability was highly variable at the southern extent of the range, particularly off the California coast, and was largely driven by habitat contractions associated with warm-water conditions. Study results provide insights into the habitat and range-wide distribution of an at-risk estuarine-reliant forage fish and are the first step toward identifying processes that affect the marine portion of the Longfin Smelt life cycle.

The location of estuarine organisms varies based on geophysical cycles and environmental conditions, which can strongly bias understanding of organism abundance and distribution. In the San Francisco Estuary, California, extensive monitoring surveys have provided insight into the life history and ecology of certain commercially important or legislatively protected fish species. However, there remains substantial uncertainty in factors influencing the vertical and lateral distributions of many other nekton species in the San Francisco Estuary, including longfin smelt Spirinchus thaleichthys, for whom such distributional information may highly influence interpretation of existing data. We carried out paired sampling using surface and demersal gears to address three questions: (1) Does diel phase influence the vertical position of nekton (e.g., surface versus demersal)? (2) Do environmental conditions, specifically turbidity, influence the vertical and lateral positions of nekton (e.g., center channel versus peripheral shoal)? (3) Does tidal variability influence vertical and lateral distributions of nekton? We documented variability in sampled nekton densities across diel phase (day/night), vertical position (surface/bottom), and lateral position (channel/shoal). Tidal phase and turbidity concentration influenced vertical and lateral distributions for some species at certain locations. Although infrequently encountered, we documented associations of longfin smelt with the lower water column and shoal habitats, with some evidence for upward vertical shifts in low light conditions brought about by nightfall or elevated turbidity. Observed habitat associations provide insight into how interacting geophysical and environmental factors may influence the distribution of nekton and thus the vulnerability of individual species to detection by sampling gears.

Water diversions that support agricultural and municipal use result in fish mortality through entrainment and impingement. Additionally, this infrastructure may attract both predators and prey fishes, thereby increasing predation rates and prey mortality near these anthropogenic contact points. The Sacramento-San Joaquin Delta (the Delta) in California's Central Valley is a tidal freshwater ecosystem that exports large volumes of water for municipal and agricultural use while at the same time providing valuable migratory and rearing habitat for imperilled fishes. Emigrating juvenile salmonids experience high mortality in the Delta, with predation by non-native fishes contributing substantially. Therefore, this study had three main objectives. First, we determined if small water diversions aggregated piscivorous fishes like other similar structures in freshwater ecosystems. Second, we determined how small diversions may influence juvenile salmon predation risk in conjunction with other known predation risk factors (e.g. predator abundance, temperature and depth). Third, we assessed the predator assemblage, abundance and distribution to determine the likely predator composition in objectives one and two. Throughout the spring of 2021, we used ARIS (adaptive resolution imaging sonar; Sound Metrics) sonars to compare piscivore abundance at 30 water diversions in the north Delta to shorelines adjacent to diversions that did not contain these structures. We used predation event recorders (PERs) to assess the predation risk juvenile salmonids were exposed to, with linear distance (m) from diversions, and other predation risk factors in the north Delta. Finally, we used a boat electrofishing survey to determine the piscivore assemblage and compare spatial trends in black bass (Micropterus spp.) CPUE and relative abundance throughout these waterways. Piscivore abundance was greater near small water diversions than at adjacent shorelines and the predation risk of juvenile salmonids increased with diversion proximity. Additionally, predation risk increased with increasing piscivore abundance and decreasing water depth. The north Delta predator assemblage was dominated by black basses (Micropterus spp.), which likely drove the negative relationship of predation risk with water depth, given habitat requirements of these species. Furthermore, increasing smallmouth (Micropterus dolomieu) and spotted bass (Micropterus punctulatus) abundance in our northern study sites may have weakened temperature effects on predation, given metabolic requirements of these species. Our work demonstrated that small water diversions are likely to increase mortality of endangered salmonids, and that the north Delta predator assemblage was different than recorded by previous work in this system, changing predation risk factors. Although more work is needed to determine the population level impacts of diversions, the ubiquitous distribution of these structures warrants management solutions to reduce mortality from this source. These results indicate that in addition to entrainment and impingement, water diversions may increase mortality of small-bodied fishes by attracting predators and elevating predation risk. Given the continual human demand for freshwater, predator-prey interactions should be considered along with entrainment and impingement when assessing intake infrastructure mitigation, especially when diversions co-occur along migratory routes and essential habitat of imperilled fishes.

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.

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.

Ecological disturbances such as fish kills can negatively impact ecosystem processes in coastal lagoons. To gain an understanding of factors causing fish kills, we examined conditions associated with a summertime fish kill in a northeastern Pacific coastal lagoon (Rodeo Lagoon, CA, USA). Examination of available data indicated the fish kill was likely caused by hypoxia involving the following etiology: (1) strong onshore winds (up to 12 m/s) mixed a stratified water column, (2) water column mixing transported nutrients from near the bed into the photic zone, (3) increased nutrient concentrations in the photic zone (> 200%) together with high solar irradiance fueled a phytoplankton bloom, (4) death and decomposition of phytoplankton (72% decrease in abundance) contributed to biological oxygen demand that led to (5) hypoxic conditions (as low as 0.6 mg/L) that caused the fish kill. The event resulted in the death of an estimated 3677 Tidewater Goby ( Eucyclogobius newberryi ), a species listed as endangered under the US Endangered Species Act, and numerous (but not enumerated) Threespine Stickleback ( Gasterosteus aculeatus ), unidentified sculpins (Cottidae), and macroinvertebrates (primarily Amphipoda). The processes contributing to the event are likely re-occurring phenomena responsible for observed periodic fish kills. Coastal lagoons with limited freshwater inflows and connection to the Pacific Ocean may retain nutrients and be susceptible to similar events.

Substantial increases in non-native aquatic vegetation have occurred in the upper San Francisco Estuary over the last 2 decades, largely from the explosive growth of a few submerged and floating aquatic plant species. Some of these species act as ecosystem engineers by creating conditions that favor their further growth and expansion as well as by modifying habitat for other organisms. Over the last decade, numerous studies have investigated patterns of expansion and turn-over of aquatic vegetation species; effects of vegetation on ecosystem health, water quality, and habitat; and effects of particular species or communities on physical processes such as carbon and sediment dynamics. Taking a synthetic approach to evaluate what has been learned over the last few years has shed light on just how significant aquatic plant species and communities are to ecosystems in the Sacramento-San Joaquin Delta. Aquatic vegetation affects every aspect of the physical and biotic environment, acting as ecosystem engineers on the landscape. Furthermore, their effects are constantly changing across space and time, leaving many unanswered questions about the full effects of aquatic vegetation on Delta ecosystems and what future effects may result, as species shift in distribution and new species are introduced. Remaining knowledge gaps underlie our understanding of aquatic macrophyte effects on Delta ecosystems, including their roles and relationships with respect to nutrients and nutrient cycling, evapotranspiration and water budgets, carbon and sediment, and emerging effects on fish species and their habitats. This paper explores our current understanding of submerged and floating aquatic vegetation (SAV and FAV) ecology with respect to major aquatic plant communities, observed patterns of change, interactions between aquatic vegetation and the physical environment, and how these factors affect ecosystem services and disservices within the upper San Francisco Estuary.

Estuarine food webs are complex, as marine, freshwater, and terrestrial inputs combine and contribute variable amounts of organic material. Seasonal fluctuations in precipitation amplify the dynamism inherent to estuarine food webs, particularly in lagoonal estuaries, which can be seasonally closed and disconnected from the ocean in low-runoff periods (bar-built lagoons). Despite their abundance along coastlines in Mediterranean climates, the organic matter sources fueling bar-built lagoon food webs are poorly understood, particularly with respect to seasonal hydrologic variability, episodic marine connections, and internal nutrient cycling. In this study, we evaluate the food web of a bar-built lagoon with respect to seasonal differences in lagoon water quality, the sources of organic matter which support consumers, and the trophic ecology of resident fishes. Observed water quality conditions reflected biogeochemical processes associated with salinity-driven stratification and high lagoon residence times and were associated with strong seasonal differences in the contribution of different organic matter sources to lagoon consumers. A variety of organic matter sources supported consumers; marine inputs were important to lagoon food webs in spring when the lagoon was open, while summer food webs were largely driven by phytoplankton which was likely fueled by internal nutrient cycling. Fish diets were largely comprised of crustaceans and fish eggs, with clearly defined trophic niches in spring but high overlap in summer. This study demonstrates that the seasonal changes in bar-built lagoon food webs are largely dependent on ocean connectivity and internal cycling within the lagoon, rather than watershed processes as is typical for many estuaries.

Stable isotopes recorded in fish eye lenses are an emerging tool to track dietary shifts coincident with use of diverse habitats over the lifetime of individuals. Eye lenses are metabolically inert, sequentially deposited, archival tissues that can open avenues to chronicle contaminant exposures, diet histories, trophic dynamics and migratory histories of individual fishes. In this study, we demonstrated that trophic histories reconstructed using eye lenses can resolve key uncertainties regarding diet and trophic habitat shifts. Clear Lake hitch (Lavinia exilicauda chi), a threatened cyprinid, inhabits a single lake (Clear Lake, Lake County, California) and utilizes tributary streams for reproduction. Bayesian mixing models applied to δ13C and δ15N recorded in eye lenses uncovered ontogenetic diet shifts that corresponded with shifts in occupation of habitats providing spawning (tributary streams), rearing (littoral lake), and growth (pelagic lake) functions. The reconstruction of size-structured trophic and habitat information can provide vital information needed to manage and conserve imperiled species such as the Clear Lake hitch.

Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restoration actions that reverse habitat loss, can modify relationships between non-native predators and prey. Predicting how these relationships will change is often difficult because insufficient information exists on the habitat-specific feeding ecology of non-native predators. To address this information gap, we examined diets of non-native Striped Bass (Morone saxatilis; 63–671 mm standard length; estimated age 1–5 y) in the San Francisco Estuary during spring and summer in three habitat types—marsh, shoal, and channel—with the marsh habitat type serving as a model for ongoing and future restoration. Based on a prey-specific index of relative importance, Striped Bass diets were dominated by macroinvertebrates in spring and summer (amphipods in spring, decapods and isopods in summer). In spring, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin (Cottus asper) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~ 40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly because of the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.