The cenotes of the Yucatan Peninsula are characterized by karstic relief, warm temperatures, and transparency of their water bodies. The mixture of fresh water from infiltrations of rainwater and runoff coupled with underground rivers or marine intrusion, make up the habitat of aquatic, amphibian, and terrestrial species. The Chen ha cenote, located in Chocholá, was used for tourist purposes, however, the lack of an environmental culture and some anthropogenic activities cause deterioration and contamination of the wetland, which putting its conservation at risk. The objective of the present work was to carry out a limnological analysis in Cenote Chen ha, to determine the level of fragility of the ecosystem. The variables analyzed were pH, dissolved oxygen, temperature, conductivity and phytoplankton biodiversity. Results. 2600 µS/cm of conductivity, 8.25 pH and 2.8 ppm of dissolved Oxygen. Phytoplankton: Diatoms 46.2%, Cyanobacteria 38.1%, Chlorophytes 8.1%, Euglenas 5.5%, and Dinoflagellates 2.1% predominated. Asterionella was identified as an indicator species of environmental health. Microcystis aureginosa, Planktothrix agardhii, and Cyanosarcina caribeana, Pseudanaena, Peridium and Gonyaulax species are shown as indicators of environmental contamination. No dominance of any species was observed; however, frequent monitoring of indicator species is recommended.