The exchange of organisms and energy among ecosystems has major impacts on food web structure and dynamics, yet little is known about how climate warming combines with other pervasive anthropogenic perturbations to affect such exchanges. We used an outdoor freshwater mesocosm experiment to investigate the interactive effects of warming, eutrophication, and changes in top predators on the flux of biomass between aquatic and terrestrial ecosystems. We demonstrated that predatory fish decoupled aquatic and terrestrial ecosystems by reducing the emergence of aquatic organisms and suppressing the decomposition of terrestrial plant detritus. In contrast, warming and nutrients enhanced cross-ecosystem exchanges by increasing emergence and decomposition, and these effects were strongest in the absence of predators. Furthermore, we found that warming advanced while predators delayed the phenology of insect emergence. Our results demonstrate that anthropogenic perturbations may extend well beyond ecosystem boundaries by influencing cross-ecosystem subsidies. We find that these changes are sufficient to substantially impact recipient communities and potentially alter the carbon balance between aquatic and terrestrial ecosystems and the atmosphere.