This study characterized water quality at sites of preference of the West Indian manatee ( Thrichechus manatus ) in the Cienaga of Paredes, an area recognized as of great ecological importance for the establishment of the species within the Middle Magdalena of Santander state (Colombia). From previous work and structured interviews eight locations were identified of which four sites were selected: Los Pozos, La Chorola and Quebrada La Gomez for greater sighting reports for shelter and food and the Punta del Roblar site for reproductive activities. The environmental quality of these sites was assessed using the physicochemical index ICA and biological BMWP / col both agree that the site with the worst water quality corresponds to the Quebrada Gomez with acceptable and very critical appraisals, respectively; the other sites were very similar to this assessment. The results of the analysis of repeated measures (ANOVA) showed no significant differences between these, but did find differences between seasons with the lowest value assigned to the last month of the year of sampling (ICA X = 0.62 ± 0.15). Continuous monitoring of the environmental conditions of Manatee habitat is urgent, to allow us to obtain an adequate understanding of the relationship between ecosystem health and animal health, in order to establish management strategies that contribute to the conservation of the species at the regional scale.