Well, the current natives (Mayas) don´t care, they use these cenotes for fun, barbecues, booze parties etc. It was only sacred for the Old Mayas. Fortunately, many of these cenotes (there are actually thousands of them on Yucatan) have some strict rules imposed to protect the unique and very fragile ecosystems that they often host. In some cenotes, many fish species, turtles, crabs and even crocodiles live ;) With your interest in wildlife and history, I think you would love these places ;)