The establishment of exotic game fishes to enhance recreational fisheries through authorized and unauthorized stocking into freshwater systems is a global phenomenon. Stocked fishes are often top predators that either replace native top predators or increase the species richness of top predators. Many direct effects of stocking have been documented, but the ecosystem consequences are seldom quantified. New studies increasingly document how species and community shifts influence ecosystem processes. We discuss here how predator stocking might increase top-down effects, alter nutrient cycles and decrease links between aquatic and surrounding terrestrial ecosystems. As fisheries management moves beyond species-specific utilitarian objectives to incorporate ecosystem and conservation goals, ecologists must address how common management practices alter food-web structure and subsequent ecosystem-level effects.