Large dams degrade the integrity of a wide variety of ecosystems, yet direct downstream effects of dams have received the most attention from ecosystem managers and researchers. We investigated indirect upstream effects of dams resulting from decimation of migratory freshwater shrimp and fish populations in Puerto Rico, USA, in both high- and low-gradient streams. In high-gradient streams above large dams, native shrimps and fishes were extremely rare, whereas similar sites without large dams had high abundances of native consumers. Losses of native fauna above dams dramatically altered their basal food resources and assemblages of invertebrate competitors and prey. Compared to pools in high-gradient streams with no large dams, pool epilithon above dams had nine times more algal biomass, 20 times more fine benthic organic matter (FBOM), 65 times more fine benthic inorganic matter (FBIM), 28 times more carbon, 19 times more nitrogen, and four times more non-decapod invertebrate biomass. High-gradient riffles upstream from large dams had five times more FBIM than did undammed riffles but showed no difference in algal abundance, FBOM, or non-decapod invertebrate biomass. For epilithon of low-gradient streams, differences in basal resources between pools above large dams vs. without large dams were considerably smaller in magnitude than those observed for pools in high-gradient sites. These results match previous stream experiments in which the strength of native shrimp and fish effects increased with stream gradient. Our results demonstrate that dams can indirectly affect upstream free-flowing reaches by eliminating strong top-down effects of consumers. Migratory omnivorous shrimps and fishes occur throughout the tropics, and the consequences of their declines upstream from many tropical dams are likely to be similar to those in Puerto Rico. Thus, ecological effects of migratory fauna loss upstream from dams encompass a wider variety of species interactions and biomes than the bottom-up effects (i.e., elimination of salmonid nutrient subsidies) recognized for northern temperate systems.