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While extreme climatic events (ECEs) are predicted to become more frequent, reliably predicting their impacts on consumers remains challenging, particularly for large consumers in marine environments. Many studies that do evaluate ECE effects focus primarily on direct effects, though indirect effects can be equally or more important. Here, we investigate the indirect impacts of the 2011 “Ningaloo Niño” marine heatwave ECE on a diverse megafaunal community in Shark Bay, Western Australia. We use an 18‐year community‐level data set before (1998–2010) and after (2012–2015) the heatwave to assess the effects of seagrass loss on the abundance of seven consumer groups: sharks, sea snakes (multiple species), Indo‐pacific bottlenose dolphins (Tursiops aduncus), dugongs (Dugong dugon), green turtles (Chelonia mydas), loggerhead turtles (Caretta caretta), and Pied Cormorants (Phalacrocorax spp.). We then assess whether seagrass loss influences patterns of habitat use by the latter five groups, which are under risk of shark predation. Sharks catch rates were dominated by the generalist tiger shark (Galeocerdo cuvier) and changed little, resulting in constant apex predator density despite heavy seagrass degradation. Abundances of most other consumers declined markedly as food and refuge resources vanished, with the exception of generalist loggerhead turtles. Several consumer groups significantly modified their habitat use patterns in response to the die‐off, but only bottlenose dolphins did so in a manner suggestive of a change in risk‐taking behavior. We show that ECEs can have strong indirect effects on megafauna populations and habitat use patterns in the marine environment, even when direct effects are minimal. Our results also show that indirect impacts are not uniform across taxa or trophic levels and suggest that generalist marine consumers are less susceptible to indirect effects of ECEs than specialists. Such non‐uniform changes in populations and habitat use patterns have implications for community dynamics, such as the relative strength of direct predation and predation risk. Attempts to predict ecological impacts of ECEs should recognize that direct and indirect effects often operate through different pathways and that taxa can be strongly impacted by one even if resilient to the other.

Within oligotrophic ecosystems, resource limitations coupled with interspecific variation in morphology, physiology, and life history traits may lead to niche partitioning among species. How generalist predators partition resources and their mechanisms, however, remain unclear across many ecosystems. We quantified niche partitioning among upper trophic level coastal and estuarine species: American alligators (Alligator mississippiensis), bull sharks (Carcharhinus leucas), common bottlenose dolphins (Tursiops truncatus), common snook (Centropomus undecimalis), and Atlantic tarpon (Megalops atlanticus) in the Shark River Estuary of the Florida Coastal Everglades, USA using acoustic telemetry, stable isotope analysis, and visual surveys, combined with published diet and life history demographic information. Spatial and isotopic niche overlap occurred among most species, with variability in partitioning among interspecific interactions. However, seasonal variability in habitat use, movements patterns, and trophic interactions may promote coexistence within this resource-limited estuary. Beyond guild-level niche partitioning, predators within the Shark River Estuary also exhibit partitioning within species through individual specializations and divergent phenotypes, which may lead to intraspecific variability in niche overlap with other predators. Niche differentiation expressed across multiple organizational levels (i.e., populations and communities) coupled with behavioral plasticity among predators in oligotrophic ecosystems may promote high species diversity despite resource limitations, which may be important when species respond to natural and human-driven environmental change.

Large predators often play important roles in structuring marine communities. To understand the role that these predators play in ecosystems, it is crucial to have knowledge of their interactions and the degree to which their trophic roles are complementary or redundant among species. We used stable isotope analysis to examine the isotopic niche overlap of dolphins Tursiops cf. aduncus, large sharks (>1.5 m total length), and smaller elasmobranchs (sharks and batoids) in the relatively pristine seagrass community of Shark Bay, Australia. Dolphins and large sharks differed in their mean isotopic values for δ 13 C and δ 15 N, and each group occupied a relatively unique area in isotopic niche space. The standard ellipse areas (SEAc; based on bivariate standard deviations) of dolphins, large sharks, small sharks, and rays did not overlap. Tiger sharks Galeocerdo cuvier had the highest δ 15 N values, although the mean δ 13 C and δ 15 N values of pigeye sharks Carcharhinus amboinensis were similar. Other large sharks (e.g. sicklefin lemon sharks Negaprion acutidens and sandbar sharks Carcharhinus plumbeus) and dolphins appeared to feed at slightly lower trophic levels than tiger sharks. In this seagrass-dominated ecosystem, seagrassderived carbon appears to be more important for elasmobranchs than it is for dolphins. Habitat use patterns did not correlate well with the sources of productivity supporting diets, suggesting that habitat use patterns may not necessarily be reflective of the resource pools supporting a population and highlights the importance of detailed datasets on trophic interactions for elucidating the ecological roles of predators.