Although the park was created to safeguard its historical significance, its almost 50.000 hectares of coastline, plains and hills serve to protect 115 mammal species 100 species of amphibians and reptiles, 253 species of birds and over 10.000 species of insects, including some 3,200 butterflies and moths.  The most attractive mammals are the white-tailed deer, which abound in the area of Santa Elena Bay, together with the white-nosed coati, howler and white-faced capuchin monkeys and collared peccary.  Some mammals, such as the jaguar, cougar and tapir, are in danger of extinction.  The tropical dry forests and mangrove swamps provide a refuge for magpie jays, perhaps the most typical bird in the Guanacaste Province, as well as for elegant trogons, orange-fronted parakeets, great curassows and common black-hawks, among other species.

Olive ridley, hawksbill, green and leatherback turtles lay their eggs on the beaches of the park.  The olive ridley turtles (from August to December) use Nancite Beach, a scenic spot on the southern tip of the Santa Elena Peninsula,) when they arrive in massive numbers.  The largest arribadas of olive ridley turtles in all of Tropical America take place at Nancite, and also at Ostional Beach on the Nicoya Peninsula.