The park is located in north-eastern Cuba and covers most of the central part of the Saqua-Baracpa mountain range. The site includes a complex system of mountains, tablelands, coastal plains, bays and coral reefs. In particular, coastal plains represent the highest and elongated system of plateaus and watersheds in the Caribbean region, with large weathering crusts and karstic or pseudo-karstic geological formations. The site includes the block of Farallones de Moa, a geological and biogeographic 'island' composed of basic and ultra-basic serpentine rocks. This contains the karstic system of Farallones de Moa Great Cavern. Several rivers flow from the park, including the Toa-Jaguani, Duaba, Jiguani, Nibujon and Moa.
The site has the highest plant diversity of the Cuban archipelago and the insular Caribbean. The park is also considered as the least explored natural area in Cuba and there still are locations from where a collection has never been made. The terrestrial vegetation contains 16 of the 28 plant formations for Cuba, including low-altitude, submontane and montane rainforest, cloud forest, xenomorphic sub-thorny shrub, pine forests, semi-deciduous forest, riverine forest and mangrove forest. Many of the underlying rocks are toxic to plants, so species have had to adapt to survive in these hostile conditions. This unique process of evolution has resulted in the development of many new species.
The park has a flora list of 1,302 spermatophytes and 145 species of pteridophytes, of which 905 species are endemic to Cuba, representing almost 30% of all endemics reported for the country. Of this total figure, 343 species live exclusively in this area. The local flora includes five species of carnivore plant, one of which is Pinguicola lignicola, the only Cuban epiphyte. There are also two endemic species of the genera Podocarpus and Dracaena. According to recent collections, five new species to science have been made in the region, one of which is a pine. A species of the genus Buxus (reported as extinct) was found in the area too. At least 30% of the mammals, 21% of the birds, 83.3% of the reptiles, 95.8% of the amphibians and 27.7% of the insects are local or national endemisms. The area is of particular importance for several species are of particular conservation concern, notably the ivory-billed woodpecker (Campephilus principalis bairdii), thought to be extinct, the Cuban kite, an endemic species whose population has been so reduced that maybe just a few couples remain, and the Cuban solenodon. Forests in the region are important as refuge for many resident and migratory bird species, such as the Cuban Amazon parrot and Cuban parakeet. With regard to reptiles, three new species of Anolis lizard have been recently collected from the park. In the marine part of the park, there are numerous colonies of Caribbean manatee.
At the beginning and middle of the 20th century, the valleys in the coast were occupied in order to raise coconut and cacao. During the 1940s and 1950s, there were some farming activities along the Toa and Jaguaní riverbanks. In the 1960s and 1970s, there was some timber exploitation, particularly of pine, in the area of Ojito de Agua. Within the park the largest human settlement is La Melba.