Among the birds there is a large number of species (over 270), the most common herons, kingfishers and ducks, among the alligators and reptiles include the black caiman, several gender of freshwater turtles, iguanas, lizards, barselicos, lizards, and reptiles, amphibians, frogs. Within mammals, is the Deer or pacas Tepeizcuintes, armadillos or armadillos, wild pigs or sorghum, coati, sloth, howler monkeys, anteaters, otters or otter, agouti bats, cats (jaguar and cinnamon) are in danger of extinction. The ichthyofauna (fish), includes Gaspar (most abundant), guapotes, bream, guabinas, snook, machaca, croaker and tilapia lately.

In the primary forest tree species such as stress Guarumo the Poroporo, La Ceiba, the Cedar Real. The area is located completely wet Ponpojoche the Helequeme the Papaturro Guabo and, in the swampy area high grasses are present as the Zacatón, the Reed, the Platanillo, the orange grove of palm trees as Yolillo, the Palma case The Corozo and wild oil palm. In the mirror of water aquatic species proliferate as water lettuce, water lily and other species.

The situation of forest resources is very critical, the dense hardwood forest is reduced to small areas (stands) are usually no larger than 50 hectares, located in the southern part Papaturro River, the south – east of the refuge near Rio Frio is devoid of its original natural flora and difficult situation for natural regeneration.

Humidity areas cover a wide range of temporary or permanent land covered with trees, palms, grasses, legumes and other emergent or floating aquatic plants where it generates, houses, feeds and organic micro immense substrate, which moves the food chain.

The fauna of the area is predominant in wild defendants for their meat and skins. The fauna of the rivers is rich in species for local consumption and international market, the variety of flora and fauna of the area tends to disappear without a sound managementand control them.

Fish: Gaspar, sea bass, croaker, lizard, , sunfish, turtle, guapotes, harriers, sawfish, sharks, tarpon, pound, sardines, tilapia, lobster.

Birds: macaws, parrots, parrots, parakeets, toucans, belts, hawk, vulture, quenquen, herons, Garson, Martin Peña, chachalacas sparrows, turkeys, peacocks, quail, guises, sensontles, save ravines, woodpeckers, grackles, etc. curlews.

Reptiles: green and black iguanas, lizards, guajipal, snakes, (velvet, coral, snake blood, bell) a lot of snakes and reptiles.

Other Types: Deer, peccaries (Sahin), armadillo, rabbit, tiger, ocelot, lions, coatis, raccoons, bobcat, squirrels, foxes, skunks, etc.

San Juan de Nicaragua, has within its plain the tropical wet forest, which is characterized by dense, evergreen giant milties traficado and lianas.

The flora of this system is one of the richest, highlighting the male cedar, laurel, mahogany, almond, rubber and oak.

Fruit: mango, orange (sweet and sour) lemons (sweet castilla, lemon, mandarin, sweet lemons) guava, cashew, cauliflower, coconut, loquat, avocado, mandarin, ICAC, breadfruit.

There are basic conditions for environmental protection by the Ministry of Environment and Natural Resources.