Estuaries are highly variable environments where fish are subjected to a diverse suite of habitat features (e.g., water quality gradients, physical structure) that filter local assemblages from a broader, regional species pool. Tidal, climatological, and oceanographic phenomena drive water quality gradients and, ultimately, expose individuals to other habitat features (e.g., stationary physical or biological elements, such as bathymetry or vegetation). Relationships between fish abundances, water quality gradients, and other habitat features in the Sacramento-San Joaquin Delta were examined as a case example to learn how habitat features serve as filters to structure local assemblages in large river-dominated estuaries. Fish communities were sampled in four tidal lakes along the estuarine gradient during summer-fall 2010 and 2011 and relationships with habitat features explored using ordination and generalized linear mixed models (GLMMs). Based on ordination results, landscape-level gradients in salinity, turbidity, and elevation were associated with distinct fish assemblages among tidal lakes. Native fishes were associated with increased salinity and turbidity, and decreased elevation. Within tidal lakes, GLMM results demonstrated that submersed aquatic vegetation density was the dominant driver of individual fish species densities. Both native and non-native species were associated with submersed aquatic vegetation, although native and non-native fish populations only minimally overlapped. These results help to provide a framework for predicting fish species assemblages in novel or changing habitats as they indicate that species assemblages are driven by a combination of location within the estuarine gradient and site-specific habitat features.

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.

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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.

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.

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.

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.

Largemouth Bass (Micropterus salmoides) were introduced into the Sacramento-San Joaquin Delta (the Delta) over 100 years ago. In the last 2 decades, the abundance of centrarchids (including Largemouth Bass) in the littoral zone has increased, while some native fish and fish that were previously abundant in the pelagic zone have declined. Largemouth Bass are now one of the most abundant piscivores in the Delta. Understanding the ecology of this top predator — including a comprehensive understanding of what prey are important in Largemouth Bass diets — is important to understanding how this species may affect the Delta fish community. To address this need, we conducted electrofishing surveys of Largemouth Bass at 33 sites every 2 months from 2008 to 2010, measuring fish fork lengths and collecting stomachs contents at each site. We characterized diets using Percent Index of Relative Importance for 3,004 Largemouth Bass, with samples that spanned all seasons. Amphipods dominated the diets of Largemouth Bass ≤175 mm FL year-round, with dipterans, odonates, and copepods and cladocerans representing other important diet items. Non-native red swamp crayfish (Procambarus clarkii) were the most important prey for Largemouth Bass >175 mm FL. Non-native centrarchids (including Largemouth Bass) and amphipods were important prey items as well. Prickly Sculpin (Cottus asper) were the most frequently consumed native fish. Other native fish and pelagic fish species rarely occurred in Largemouth Bass diets, and we discuss trends in how the frequency of co-occurrence of these fishes with Largemouth Bass in the electrofishing surveys was associated with their frequency in Largemouth Bass diets. The Largemouth Bass in the Delta appear to be sustained largely on a diet of other non-natives that reside in the littoral zone.