The marshy lagoons provide feeding, nesting and rest sites for species of waterfowl and wading birds, especially during the dry season (December - May) when there are concentrations of up to 20.000 black-bellied tree ducks, 25.000 blue winged- teals, 4.000 wood storks and 700 roseate spoonbills.  It is estimated that there are 300 species of land birds and waterfowl.  On the 2.3 hectares of the small floating Pájaros Island there are no less than 11 species of wading birds ant the largest colony of black-crowned night herons in the country.

There are the least 12 and probably as many 15 habitats within the park, which range from the steep slopes and limestone mountain ranges to the banks of the Rivers Tempisque and Bebedero.  These include saltwater and freshwater lagoons and marshes, mangrove swamps, swamp forest, evergreen forest, deciduous savannah woodland, hillside mixed forest, grassland of rough-leaf tree and riparian forest.

Average annual rainfall in this climate is 1,500-2,000 mm., with the heaviest rains falling in September and October, the season when the rivers overflow.  The network that waters the park flows down from the Guanacaste Mountain Range and the Nicoya Peninsula to the Tempisque basin, the main collector that together with the River Bebedero waters 11% on the territory of Costa Rica.