Investigating the effects of climatic variability on biological diversity, productivity, and stability is key to understanding possible futures for ecosystems under accelerating climate change. A critical question for estuarine ecosystems is, how does climatic variability influence juvenile recruitment of different fish species and life histories that use estuaries as nurseries? Here we examined spatiotemporal abundance trends and environmental responses of 18 fish species that frequently spend the juvenile stage rearing in the San Francisco Estuary, CA, USA. First, we constructed multivariate autoregressive state-space models using age-0 fish abundance, freshwater flow (flow), and sea surface temperature data (SST) collected over four decades. Next, we calculated coefficients of variation (CV) to assess portfolio effects (1) within and among species, life histories (anadromous, marine opportunist, or estuarine dependent), and the whole community; and (2) within and among regions of the estuary. We found that species abundances varied over space and time (increasing, decreasing, or dynamically stable); and in 83% of cases, in response to environmental conditions (wet/dry, cool/warm periods). Anadromous species responded strongly to flow in the upper estuary, marine opportunist species responded to flow and/or SST in the lower estuary, and estuarine dependent species had diverse responses across the estuary. Overall, the whole community when considered across the entire estuary had the lowest CV, and life histories and species provided strong biological insurance to the portfolio (2.4- to 3.5-fold increases in stability, respectively). Spatial insurance also increased stability, although to a lesser extent (up to 1.6-fold increases). Our study advances the notion that fish recruitment stability in estuaries is controlled by biocomplexity-life history diversity and spatiotemporal variation in the environment. However, intensified drought and marine heatwaves may increase the risk of multiple consecutive recruitment failures by synchronizing species dynamics and trajectories via Moran effects, potentially diminishing estuarine nursery function.

Climate change is intensifying the effects of multiple interacting stressors on aquatic ecosystems worldwide. In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems: anadromous Chinook Salmon (Oncorhynchus tshawytscha) and estuarine resident Sacramento Splittail, (Pogonichthys macrolepidotus). Based on our review, we found that the estuary is experiencing shifting baseline environmental conditions, amplification of extremes, and restructuring of physical habitats and biological communities. We present priority topics for research and monitoring, and a conceptual model of how the estuary currently functions in relation to climate variables. In addition, we discuss four tools for management of climate change effects: regulatory, water infrastructure, habitat development, and biological measures. We conclude that adapting to climate change requires fundamental changes in management.

Mechanisms driving the consumption and transport of tidal marsh nutrients and energy by fishes are of key interest in the San Francisco Estuary, CA, USA. By combining multiple data sources (gill-net catches, gut contents, channel morphology, tides), we modeled spatial and temporal patterns of fish abundance and gut fullness across a tidal marsh elevation gradient. Channel depth, microhabitat, and tide were important predictors of fish abundance and gut fullness. Species, feeding guild, and season were also important to fish abundance but not to gut fullness, suggesting that abundance was more related to physical constraints of shallow water than to prey availability. Multiple feeding guilds overlapped in space and time at interaction hotspots in subtidal channel habitat near the marsh entrance. In contrast, fish use of shallow intertidal marsh channels was more variable and indicated tradeoffs between foraging and predation. Gut content analysis revealed moderate-to-high gut fullness for all feeding guilds and models predicted high gut fullness in subtidal reaches during tidal flooding, after which fish fed intensively throughout the marsh. While mysids, amphipods, and detritus were common prey among feeding guilds, variation in prey consumption was apparent. Overall, complex tidal marsh hydrogeomorphology driving land-water exchange and residence time may diversify and enhance benthic and pelagic food web pathways to fishes and invertebrates. Furthermore, these findings substantiate the notion that dynamic tidal marshes in this system can support robust secondary production, foraging by multiple feeding guilds, and trophic transfer by fishes to the estuarine mosaic.

Little is known about the ecological importance of low-order tidal marsh channels to fishes in the San Francisco Estuary, California. We conducted a passive mark-recapture study to compare residency, site fidelity, and movement patterns of fishes in a small intertidal channel (0.1 km2) in a large tidal marsh reserve (4.25 km2). We coupled continuous, high-frequency data on movements of fish tagged with Passive Integrated Transponder (PIT) tags and abiotic conditions from a PIT-detector and datasonde, respectively. Novel insights were gained by employing TidalTrend, a software program that characterizes tidal time-series data for ecological interpretation. Overall, we found that fishes exhibited different patterns of intertidal habitat use: the resident species, tule perch (Hysterocarpus traski), consistently spent more time per visit, per day, and per season using the intertidal channel, except during the reproductive window in spring; the transient species, Sacramento splittail (Pogonichthys macrolepidotus) and striped bass (Morone saxatilis), were more opportunistic and exhibited higher individual variation in movement patterns. Generalized additive mixed models indicated that tide height, rate of change in tide height, tidal inequality, time of day, lunar phase, and water temperature better predicted fish detections than other variables, but their effects varied across species. Based on our findings, we posit that time, through tides, allows habitat partitioning among fish species and individuals with different life-history types. Furthermore, functional connectivity between subtidal and intertidal channels in tidal marshes is a feature of the estuarine mosaic that should be integrated into habitat restoration designs in the San Francisco Estuary.

Ecosystem management and governance of cross-scale dependent systems require integrating knowledge about ecological connectivity in its multiple forms and scales. Although scientists, managers, and policymakers are increasingly recognizing the importance of connectivity, governmental organizations may not be currently equipped to manage ecosystems with strong cross-boundary dependencies. Managing the different aspects of connectivity requires building social connectivity to increase the flow of information, as well as the capacity to coordinate planning, funding, and actions among both formal and informal governance bodies. We use estuaries in particular the San Francisco Estuary, in California, in the United States, as examples of cross-scale dependent systems affected by many intertwined aspects of connectivity. We describe the different types of estuarine connectivity observed in both natural and human-affected states and discuss the human dimensions of restoring beneficial physical and ecological processes. Finally, we provide recommendations for policy, practice, and research on how to restore functional connectivity to estuaries.

Tidal marshes are a key component of coastal seascape mosaics that support a suite of socially and economically valuable ecosystem services, including recreational opportunities (e.g., fishing, birdwatching), habitat for fisheries species, improved water quality, and shoreline protection. The capacity for tidal marshes to support these services is, however, threatened by increasingly widespread human impacts that reduce the extent and condition of tidal marshes across multiple spatial scales and that vary substantially through time. Climate change causes species redistribution at continental scales, changes in weather patterns (e.g., rainfall), and a worsening of the effect of coastal squeeze through sea level rise. Simultaneously, the effects of urbanization such as habitat loss, eutrophication, fishing, and the spread of invasive species interact with each other, and with climate change, to fundamentally change the structure and functioning of tidal marshes and their food webs. These changes affect tidal marshes at local scales through changes in plant community composition, complexity, and condition and at regional scales through changes in habitat extent, configuration, and connectivity. However, research into the full effects of these multi-scaled, interactive stressors on ecosystem service provision in tidal marshes is in its infancy and is somewhat geographically restricted. This hinders our capacity to quickly and effectively curb loss and degradation of both tidal marshes and the services they deliver with targeted management actions. We highlight ten priority research questions seeking to quantify the consequences and scales of human impacts on tidal marshes that should be answered to improve management and restoration plans.

Coastal salt marshes are distributed widely across the globe and are considered essential habitat for many fish and crustacean species. Yet, the literature on fishery support by salt marshes has largely been based on a few geographically distinct model systems, and as a result, inadequately captures the hierarchical nature of salt marsh pattern, process, and variation across space and time. A better understanding of geographic variation and drivers of commonalities and differences across salt marsh systems is essential to informing future management practices. Here, we address the key drivers of geographic variation in salt marshes: hydroperiod, seascape configuration, geomorphology, climatic region, sediment supply and riverine input, salinity, vegetation composition, and human activities. Future efforts to manage, conserve, and restore these habitats will require consideration of how environmental drivers within marshes affect the overall structure and subsequent function for fisheries species. We propose a future research agenda that provides both the consistent collection and reporting of sources of variation in small-scale studies and collaborative networks running parallel studies across large scales and geographically distinct locations to provide analogous information for data poor locations. These comparisons are needed to identify and prioritize restoration or conservation efforts, identify sources of variation among regions, and best manage fisheries and food resources across the globe.

Climate change is altering naturally fluctuating environmental conditions in coastal and estuarine ecosystems across the globe. Departures from long-term averages and ranges of environmental variables are increasingly being observed as directional changes [e.g., rising sea levels, sea surface temperatures (SST)] and less predictable periodic cycles (e.g., Atlantic or Pacific decadal oscillations) and extremes (e.g., coastal flooding, marine heatwaves). Quantifying the short- and long-term impacts of climate change on tidal marsh seascape structure and function for nekton is a critical step toward fisheries conservation and management. The multiple stressor framework provides a promising approach for advancing integrative, cross-disciplinary research on tidal marshes and food web dynamics. It can be used to quantify climate change effects on and interactions between coastal oceans (e.g., SST, ocean currents, waves) and watersheds (e.g., precipitation, river flows), tidal marsh geomorphology (e.g., vegetation structure, elevation capital, sedimentation), and estuarine and coastal nekton (e.g., species distributions, life history adaptations, predator-prey dynamics). However, disentangling the cumulative impacts of multiple interacting stressors on tidal marshes, whether the effects are additive, synergistic, or antagonistic, and the time scales at which they occur, poses a significant research challenge. This perspective highlights the key physical and ecological processes affecting tidal marshes, with an emphasis on the trophic linkages between marsh production and estuarine and coastal nekton, recommended for consideration in future climate change studies. Such studies are urgently needed to understand climate change effects on tidal marshes now and into the future.