The lake area presents high levels of migration, due to the existence of natural resources such as wood, chewing gum, oil, and agricultural and pasture activities.

The city of Flores, the capital of the Petén Department, lies on an island near its southern shore.

Several streams flow into Lake Petén Itzá, but it has no surface outflow.

This lake and its surroundings have more than 100 important indigenous species such as the cichlid fish Mayaheros urophthalmus, Petenia splendida and Vieja melanurus, the endemic Poecilia petenensis, crocodiles (Crocodylus moreletii and Crocodylus acutus), jaguars (Panthera onca), pumas (Puma concolor), white-tailed deer (Odocoileus virginianus), Central American red brocket (Mazama temama), and several bird species, including parrots such as macaws, and toucans.

On its northeast shore is the Cerro Cahui Protected Biotope, a natural reserve for butterflies that covers 1,600-acre (6.5 km2) and is home to toucans, Geoffroy's spider monkey (Ateles geoffroyi), Guatemalan black howler monkeys (Alouatta pigra), and many other rainforest species.