The Lake is an important corridor for migratory birds from North, Central and South America, in which, birds live in the lake region from November to March. It has been registered 127 bird species, 57 aquatic and 70 terrestrial.
Among the migratory birds are: Great Egret (Ardea alba), White-faced Ibis (Plegadis chihi), Black-bellied Whistling-Duck (Dendrocygna autumnalis) and Caspian Tern (Hydroprogne caspia). There are four endemic species. Among those with special protection by the Official Mexican Standard are: Least Grebe (Tachybaptus dominicus), Wood Stork (Mycteria americana) and Least Bittern (Ixobrychus exilis). The emblematic specie of the lake is the Black-necked Stilt (Himantopus mexicanus). In the rest of the species, little study has been done, however there are recorded 40 species of mammals, 13 species of reptiles, 6 of amphibians and 7 of fish. Among endemic fish there are some in danger of extinction, just like: the Longjaw Silverside (Menidia grandocule); between amphibians, the Big-footed Leopard Frog (Lithobates megapoda), is a threatened species.
There are 442 vegetable species registered, however, due to the high change of land use, global warming and climate change, at this moment many of them are at risk. A dominant vegetable aquatic and endemic specie is cattail (Typha domingensis and Scirpus), which is used for local families to make crafts and everyday use items.
Lake Zapotlán is highly threatened and endangered by being in a closed basin, with a strong change in land use in buffer zones; this is due to fruit crops and a settlement of 140,000 fixed and floating people. Human settlements are composed by indigenous, rural and urban communities. So, the lake and the sub-basin of Zapotlán show high contamination of gray water and industrial waste of agrochemicals, livestock, forestry, natural waste as well as for volcanic events. There is currently manual, mechanical and biological control by the invasion of lily and cattail. Secondary treatment of urban water is also applied.