How animals respond to climate variability depends strongly on their life histories. In marine systems, mobile pelagic fishes may shift distributions to track favourable conditions, whereas more sedentary reef fishes are more likely to endure environmental impacts in place. These contrasting responses, in turn, may impact the fisheries that rely on these species. Here, we analyse fishery data spanning 63 years from 23 Western and Central Pacific Ocean (WCPO) nations to examine how pelagic and reef fishes, as well as their fisheries, have responded to a large-scale environmental phenomenon: El Niño–Southern Oscillation (ENSO). Our results show that the biomass distributions of larger, tropical pelagic fishes shifted longitudinally across the WCPO in response to ENSO. In contrast, local reef fish biomass appears to decrease during strong ENSO transitions. We also found an inverse relationship between pelagic and reef fish catch during strong ENSO transitions, consistent with artisanal and subsistence fishers switching their fishing targets to more accessible reef fishes. This pattern suggests that wild-capture fisheries possess some capacity to adapt to environmental changes. As climate variability is forecast to increase, reef fish stocks may face mounting pressure from the convergence of greater environmental stress and intensified fishing as fishers switch targets more frequently. These compounding pressures could outpace the adaptive capacity of small-scale fishers, with serious implications for the food security and livelihoods of the communities that depend on them. These dynamics are likely to characterise other climate-sensitive ocean regions where fisheries depend on species with distinct life-history strategies.