Fishes are a prominent component of animal communities in tropical freshwaters due to their high species richness, great abundance, and large size. Their contributions to the functioning of tropical freshwater ecosystems are poorly understood, but are increasingly threatened by human activities. I studied the functional importance of fishes in Lake Tanganyika, Africa, and Rio Las Marias, Venezuela. In Lake Tanganyika, I tested the interactions between top-down control by grazing fishes and bottom-up control by nutrients. Grazing fish strongly suppressed algal biomass and enhanced biomass-specific primary productivity, regardless of nutrient manipulations. Fish also influence nutrient availability indirectly by recycling dietary nitrogen (N) and phosphorus (P). I quantified nutrient excretion rates by 14 species in Lake Tanganyika and 49 species in Rio Las Marias. In each ecosystem, there was striking variation in N and especially P recycling, yielding >10-fold variation in excreted N:P ratios. Using data from extensive fish surveys, I estimated that aggregate nutrient recycling by fishes varies 8-fold among sites in Lake Tanganyika and >14-fold in Rio Las Marias. These results indicate that fish distributions in each ecosystem are sufficiently heterogeneous to engender hotspots of nutrient recycling where local nutrient availability is enhanced and dissolved N:P ratios are altered. Comparing aggregate excretion estimates to ambient nutrient concentrations and ecosystem nutrient demand indicates that recycling by fishes probably plays a critical role in supporting primary productivity in both ecosystems. To assess the potential loss of nutrient recycling resulting from erosion of fish diversity, I simulated a suite of potential extinction scenarios. A small subset of species dominated aggregate recycling, and contributions of individual species differed between N and P. The consequences of simulated extinctions varied widely among scenarios, and compensatory responses by surviving species could moderate reductions in aggregate excretion. Fisheries data from each ecosystem indicate that the species targeted by fishermen were among the most important contributors to recycling. Thus, overfishing could yield rapid declines in nutrient regeneration. Taken together, these results indicate that fishes species vary widely in their functional characteristics, and that anthropogenic alteration of tropical fish communities may have unseen feedbacks on ecosystem processes and services.