One interesting phenomenon peculiar to the Rio San Juan is the migration of bull sharks from the salt water of the Atlantic Ocean upriver to Lake Nicaragua. It's not known why these very large relatives of the great white shark make the trip, or exactly how they deal with the change of salinity so quickly. They pose no danger to travel on the river and no attacks have been recorded on it. They may be essentially extinct anyway, from overfishing near the mouth of the San Juan river and perhaps from changing conditions in the river itself.
In this park live 7 different species of tortoise.

Much of the refuge can be visited by navigating the vast network of rivers, channels and lakes that cross through it, making it easy to observe the wildlife that inhabits the banks and shores, especially waterfowl, river turtles, monkeys and sloths.

Trees found here: coconut palm, holillo palm, wild tamarind, crabwood, cativo, banak, berm, Santa Maria, bully tree, dove wood, black palm, stilt palm, suita palm, portorrico.

Some of the most common species of fish are: the gar (which is considered to be a living fossil), the tarpon, the guapote, the Caribbean snook, mackerel and snapper.

Birds found here: keel-billed toucan, great curassow, Neotropic cormorant, anhinga, great blue heron, green macaw, tricolored heron, green ibis, white hawk, sungrebe, short-billed pigeon, and red-lored amazon, white-necked jacobin

Animals found here: West Indian manatee (endangered species), tapir, cougar (endangered species), jaguar (endangered species), jaguarundi (endangered species), and ocelot (endangered species), white-lipped peccary, paca, red brocket deer, collared peccary, southern opossum, gray four-eyed opossum three-toed sloth, howler monkey, and white-faced capuchin monkey, iguana, caiman, crocodile (endangered species).