Migratory freshwater fauna depend on longitudinal connectivity of rivers throughout their life cycles. Amphidromous shrimps spend their adult life in freshwater but their larvae develop into juveniles in salt water. River fragmentation resulting from pollution, land use change, damming and water withdrawals can impede dispersal and colonization of larval shrimps. Here we review current knowledge of river fragmentation effects on freshwater amphidromous shrimp in the Neotropics, with a focus on Puerto Rico and Costa Rica. In Puerto Rico, many studies have contributed to our knowledge of the natural history and ecological role of migratory neotropical shrimps, whereas in Costa Rica, studies of freshwater migratory shrimp have just begun. Here we examine research findings from Puerto Rico and the applicability of those findings to continental Costa Rica. Puerto Rico has a relatively large number of existing dams and water withdrawals, which have heavily fragmented rivers. The effects of fragmentation on migratory shrimps’ distribution have been documented on the landscape-scale in Puerto Rico. Over the last decade, dams for hydropower production have been constructed on rivers throughout Costa Rica. In both countries, large dams restrict shrimps from riverine habitat in central highland regions; in Puerto Rico 27% of stream kilometers are upstream of large dams while in Costa Rica 10% of stream kilometers are upstream of dams. Research about amphidromy specific to non-island shrimps is increasingly important in light of decreasing hydrologic connectivity.