Noteworthy fauna includes nationally endangered amphibians and reptiles such as the Mexican Garter Snake (Thamnophis eques), the Striped Lizard (Cnemidophorus communis) and the endemic frog Rana megapoda. In the catchment area of the lagoon, a rich biodiversity is found: lizards, armadillos, coyotes, racoons, opossums and bats are living there.
The shore vegetation is characterised by forests, savannahs, semi-deserts and cultivated land. The biodiversity of the plants ranges from tropical rain forest to a multitude of flowering plants, e.g. Yellow Loosestrife.
The area around the site presents geothermal springs and is often used for recreational activities. Large amounts of water are withdrawn from the in-flows for private, industrial and cultivation uses. The water quality of the lagoon is highly threatened by pesticides from agricultural uses as well as by untreated waste water from the industry and households. Deforestation and water infrastructure works are two of the greatest threats to the integrity of the site.
