The Guaraquecaba area was long isolated because of relative inaccessibility, but this has changed in the last 30 years. A road built into the area has provided entry for ranchers, loggers, farmers and tourism development. A 1995 threats analysis named Asian water buffalo ranching as the area’s number one threat, responsible for far more forest clearing and environmental degradation than any of the other threats analyzed. Those areas not yet cleared are under imminent threat of deforestation or are damaged by unfenced buffalo herds.

Unsustainable extractive activities such as logging, heart-of-palm harvesting, overfishing, hunting and "slash-and-burn" subsistence agriculture are systematically eroding the resource base of Guaraquecaba’s rich forests. Some of the endangered species, such as the red-tailed parrot, are caught and sold into the pet trade or hunted for food. Siltation resulting from removal of the forest is clogging local rivers and bays, hindering fishing and navigation.