The West Indian manatee is divided into two subspecies, both listed as endangered. The Antillean subspecies (Trichechus manatus manatus) inhabits coastal tropical waters of Latin America and the Caribbean. Effective conservation strategies depend on understanding local habitat use, which is poorly studied in much of its range. Important habitat characteristics for manatees include availability of freshwater and vegetation, lack of strong currents, and shallow water depth. Other aspects of manatee habitat, such as benthic biotic and abiotic features, are more difficult to determine due to low water visibility. Recent studies have demonstrated that these features may be characterized using side-scan sonar. Buena Vista and San Pedro, two areas of manatee use within the Isla de la Juventud, Cuba, were characterized using side-scan sonar. The environmental complexity of both regions was measured by imaging the benthic environment and measuring water depth. Sonar images were ground-truthed visually. Additionally, freshwater sources were mapped. The number and length of creeks and channels was recorded as an indicator of the abundance of sheltered areas. Buena Vista is composed of several large, shallow lagoons, interconnected and with access to the sea by multiple channels. San Pedro is composed of two large, deeper lagoons and several smaller, very shallow lagoons. Compared to Buena Vista, San Pedro had a greater range of depth, more channels and lagoons, and access to freshwater sources. Despite the differences, both of these areas appear to be important to manatees in the region and may provide different resources (e.g. food, shelter).