Several species of amphidromous shrimp play important roles in the food webs of Neotropical freshwater stream ecosystems. We quantified the timing and magnitude of the upstream migration of 3 genera of amphidromous shrimp on the Rio Espiritu Santo in northeastern Puerto Rico. We then used multiple regression analyses to identify potential environmental factors that affected our observed migration rates. We also conducted artificial stream experiments to assess which potential physical and chemical factors affect migratory behavior. Shrimp post-larvae migration patterns and the environmental factors affecting those patterns were species specific. The migration rates of Xiphocaris elongata and Macrobrachium spp. were more affected by environmental conditions than were those of Atya spp. The migration rates of X. elongata and Macrobrachium spp. were negatively affected by high stream discharge. Atya spp. made up most of the total post-larvae migration; however, Macrobrachium spp. migration was highly seasonal and made up a large proportion of the total shrimp migration in late summer. Migration rates of all post-larvae were uniformly distributed throughout the night. Experimental increases in turbidity had a negative effect on the migratory behavior of Atya spp. and X. elongata post-larvae, as did the presence of fish predators. Our results confirm evolutionary hypotheses regarding migration cues and dynamics of diadromous species. Flow variables provide reliable cues for upstream migration pathways and allow colonization of island habitats, whereas predator-related cues (fish and light) are recognized and avoided, a pattern that suggests adaptation to predation.