In the Yucatán Peninsula, anthropogenic activities such as urbanization and final dispose of solid and wastewaters critically impact aquatic systems. Here, we evaluated the anthropogenic-related environmental alteration of Lake La Sabana, located in the northern limit of one of the main cities of the Mexican Caribbean. We evaluate lake water quality using physical, chemical, and microbiological indicators, and heavy metals in surficial sediments and fish tissue to evaluate the potential environmental risk. Multivariate analyses reveal that environmental conditions in La Sabana are spatial and temporal heterogeneous. Medium to bad water quality was determined within basins by the NSFWQI, related with the degree of anthropogenic influence. The center-south zones display critical microbiological values largely exceeding national standards. Heavy metals in sediments (Zn>Hg) and fish tissue (Hg) were relatively low, but Hg concentration threat the ecological environment. Incipient wastewater treatment and final dispose in La Sabana is the main responsible of changes in the trophic status and nutrients availability, which in turn may have promoted changes in the biological structure and aquatic plant invasions. Lake La Sabana can be considered a model of the potential sequential effects of the anthropogenic alterations in oligotrophic karts tropical aquatic systems in Yucatán Peninsula.