Freshwater migratory shrimps, an important component of tropical aquatic ecosystems, are vulnerable to land-use change during their upstream and downstream migrations. At La Selva Biological Station in the Sarapiquí region of Costa Rica, shrimp population data were collected between 1988 and 1989, before massive land-use change occurred downstream that could potentially affect shrimp recruitment upstream. Using generalized linear models and a Bayesian inference framework, the relative abundance of Macrobrachium olfersi between recent (2008–2011) and historical time periods (1988–1989) was compared in three stream reaches. Shrimp relative abundance in two stream reaches within the protected area of La Selva was relatively constant yearly and between recent post-disturbance (2008–2011) and historical pre-disturbance (1988–89) time periods. In contrast, a stream reach bordered by pasture accessible to fishermen, showed an 87% decrease in relative abundance between recent and historical time periods suggesting site-level disturbance, possibly from fishing. The lack of change between historical and contemporary sampling periods within interior-forest stream reaches suggests that shrimp populations in protected forested reaches are resistant or resilient to certain land-use changes occurring downstream.