Atlantic tarpon Megalops atlanticus is an important recreational fisheries resource in the 6 brackish water lagoons located in Puerto Rico's Humacao Natural Reserve. The lagoons, which formed on the reserve after Hurricane David and Tropical Storm Frederick flooded the area in August 1979, are arranged in series and connect to the sea during periods of substantial precipitation. Subsequently, they reflect environmental gradients from essentially marine to low-salinity brackish water conditions. From March 2000 to April 2001, experimental mesh gill nets (N = 228) were utilized to conduct stock assessments of tarpon in the lagoons. Relative abundances of tarpon were greater as isolation (i.e., distance) from the system's confluence with the sea increased. Salinity decreased and water clarity increased as the distance from the Caribbean Sea increased. Tarpon relative abundances in the lagoons tended to be related more to water clarity than to salinity.