[10][2] The reserve included wetlands[11] and protected an example of the virgin tropical moist forest that once blanketed the territory alongside the San Juan River.
[8][12] The permanently inundated swamps are home to stands of the palm Raphia taedigera and are surrounded by thickets of species in the family Melastomataceae.
[8] Dry land contains large amounts of almendro trees (Dipteryx oleifera), a favoured food source of the great green macaw, which may grow to 60m high.
Non-native trees in secondary woodland are primarily Gmelina arborea, teak Tectona grandis and Terminalia ivorensis (locally known as acacia).
[8] Endangered plants include the conifer Podocarpus guatemalensis and the trees Cedrela fissilis, Sclerolobium costarricense, Platymiscium pinnatum and Hymenolobium mesoamericanum.
[12] Lake Colpachi has the large trees Brosimum utile, Inga alba, Pentaclethra macroloba, Vochysia ferruginea and Pouteria durlandii surrounding it, interspersed with smaller trees of Alibertia atlantica, Byrsonima crispa, Casearia arborea, Cordia bicolor, Croton smithianus, C. schiedeanus, Ferdinandusa panamensis, Laetia procera, Stryphnodendron microstachyum, Vismia macrophylla and the pioneer tree species Simarouba amara, Tapirira guianensis and Jacaranda copaia in former clearings, and shrubs of Zygia confusa.
[12] Lake Maquenque is fringed with shrubs of Zygia confusa, the large herbaceous Maranthes panamensis, the shrubs Miconia punctata and Mouriri gleasoniana, the walking palm (Socratea exorrhiza), the smallish trees Virola sebifera, Byrsonima crispa, Eschweilera costaricensis and E. panamensis, and large trees of Terminalia amazonica, Pentaclethra macroloba and Vochysia ferruginea.
panamensis, Ferdinandusa panamensis, Laetia procera, Licania affinis and L. belloi, the smallish pioneer tree species Jacaranda copaia, Simarouba amara and Tapirira guianensis, the palm Socratea exorrhiza, and the shrubs Hirtella media, Miconia punctata and Mouriri gleasoniana.
[12] Fifty meters from the lakes the following plants have been recorded as food plants for the great green macaw: the palms Iriartea deltoidea, Raphia taedigera, Socratea exorrhiza and Welfia regia, the large shrub Solanum rugosum, the emergent trees Balizia elegans and Dipteryx oleifera, the trees Byrsonima crispa, Cespedesia macrophylla, Croton schiedeanus, Dialum guianense, Guarea rhopalocarpa, Laetia procera, Pentaclethra macroloba, Qualea paraensis, Sacoglottis tricogyna, Vantanea barbourii, Virola koschnyi, Virola sebifera and Vochysia ferruginea.
[8] The bobo mullet (Joturus pichardi), Brachyrhaphis olomina,[12] knife livebearer fish (Alfaro cultratus) and the tetra (Astyanax fasciatus) are quite common.
Tropical ground snakes include Trimetopon gracile, T. pliolepis, T. simile and T. viquezi, all endemics to Costa Rica.
[12] Other birds include dusky antbird (Cercomacroides tyrannina), rufescent tiger-Heron (Tigrisoma lineatum), keel-billed toucan (Ramphastos sulfuratus), Psittacara finschi parakeets,[10] scaled pigeon (Patagioenas speciosa), the doves Geotrygon violacea and G. veraguensis, the hummingbird Lophornis helenae, the threatened South American bittern (Botaurus pinnatus) and least bittern (Ixobrychus exilis), the vulnerable agami heron (Agamia agami), sunbittern (Eurypyga helias), Muscovy duck (Cairina moschata), masked duck (Nomonyx dominicus), the trogon Trogon clathratus , the quetzal Pharomachrus mocinno at higher altitudes, the green-and-rufous kingfisher (Chloroceryle inda) and the great jacamar (Jacamerops aureus) at the lowest altitudes, the motmot Hylomanes momotula, the locally threatened green ibis (Mesembrinibis cayennensis) and roseate spoonbill (Platalea ajaja), and the locally threatened tinamous Tinamus major and Crypturellus boucardi ssp.
[12] Galliformes include the vulnerable great curassow (Crax rubra), the threatened crested guan (Penelope purpurascens) and the quails Odontophorus melanotis and Rhynchortyx cinctus.
[12] Passerine birds which occur here and are rare for Costa Rica are the yellow-tailed oriole (Icterus mesomelas), tawny-chested flycatcher (Aphanotriccus capitalis), lovely cotinga (Cotinga amabilis), strong-billed woodcreeper (Xiphocolaptes promeropirhynchus); the mid-elevation brown-billed scythebill (Campylorhamphus pusillus) and long-tailed woodcreeper (Deconychura longicauda); the speckled mourner (Laniocera rufescens), Piprites griseiceps, Carpodectes nitidus and Lanio leucothorax at lower altitudes; and the three-wattled bellbird (Procnias tricarunculatus) and bare-necked umbrellabird (Cephalopterus glabricollis) usually found at higher altitudes.
[12] As of 1997 mammals included endangered manatees,[2][3] the paca Cuniculus paca,[8] the agouti Dasyprocta punctata, the squirrel Sciurus deppei, the nationally uncommon opossum Metachirus nudicaudatus, the locally endangered giant anteater (Myrmecophaga tridactyla), silky anteater (Cyclopes didactylus), the locally reduced Hoffmann's two-toed sloth (Choloepus hoffmanni), brown-throated sloth (Bradypus variegatus), the locally threatened armadillo (Cabassous centralis),[12] jaguar (Panthera onca),[3] puma (Puma concolor),[8] jaguarundi (Herpailurus yagouaroundi), margay (Leopardus wiedii), ocelot (Leopardus pardalis), cacomistle (Bassariscus sumichrasti), olingo (Bassaricyon gabbii), grison (Galictis vittata),[12] the locally endangered otter Lontra longicaudis, tapir (Tapirus bairdii), the deer Mazama americana[8] and Odocoileus virginianus,[12] and both the locally endangered white-lipped peccary and the collared peccary.