San Juan (Nicaragua/Costa Rica)




William Bussing and Scott Smith contributed material to this text.


Costa Rica

Major Habitat Type

Tropical and subtropical coastal rivers

Drainages flowing into

Caribbean Sea

Main rivers to other water bodies

The area includes eastward-flowing rivers of Nicaragua and Costa Rica, which empty into the Caribbean Sea. The San Juan ecoregion is named for the 200 km long San Juan River, which is shared by Costa Rica and Nicaragua and connects Lake Nicaragua to the Caribbean. Other rivers include Nicaragua’s Escondido, Grande de Matagalpa, and Prinzapolka, and Costa Rica’s Tortuguero, Parismina, and Matina rivers. The Nicaraguan Great Lakes (Nicaragua and Managua) are found in the western part of the ecoregion. Lake Nicaragua is the largest lake in Central America, with a surface area of approximately 8,000 km2 (elevation of 34 m asl).



The San Juan ecoregion extends southward from the Prinzapolka basin in Nicaragua to the Estrella River basin in Costa Rica. From north to south, the western boundary is marked by the Cordillera Isabella, the basins of Nicaragua’s Great Lakes, and finally the Cordillera de Guanacaste and part of the Cordillera de Talamanca.


The Cordillera Isabella reaches elevations above 1700 m in the northwest, and the Cordilleras de Guanacaste and Talamanca in the southwest reach elevations over 3000 m. Central Nicaragua has a broad lowland (Mosquito Coast) that forms one of the most extensive coastal plains in Central America (Bussing 1976). In the east the rest of the ecoregion is at or near sea level.

Freshwater habitats

The relief of the northern highlands of Nicaragua is steep and broken, and most streams are truncated and have small drainages (de la Rosa 1995). The rivers of the northwestern part of the ecoregion are short in length, generally oriented north to south, and drain into Lake Nicaragua (Lopez Medina 2002).

The ecoregion’s southern rivers originate in the Cordillera de Guanacaste and the Cordillera de Tilaran in Costa Rica. The high precipitation along the northern edge of the Cordillera de Tilaran contributes approximately 85% to the San Juan River’s total volume (Lopez Medina 2002). In Costa Rica, the rivers of the Caribbean coast are long and wide (navigable) with an abundance of water, and carry large amounts of sediments and organic material. During the rainy season, these rivers overflow.

Terrestrial habitats

The lowland moist forests that occur throughout the lower elevations of the ecoregion include the Isthmian-Atlantic moist forests in the south and Central American Atlantic moist forests in the north. Terrestrial habitats also include pine-oak forests in the northeast and Talamancan montane forests at high elevations along the central volcanic Cordillera in Costa Rica (World Wildlife Fund 2001). In the eastern foothills, gallery forests occur along rivers, and coastal forest and mangrove swamps are found along the Caribbean coast (Montenegro-Guillen 2003). Dry tropical forests surround Lake Nicaragua.

Description of endemic fishes

There are more than 15 known endemic species in the San Juan province (Smith and Bermingham 2005), of which the majority are cichlids. Other secondary fish families with endemics include Poeciliidae, Atherinopsidae, Clupeidae, Rivulidae, and Gobiidae. The ecoregion is also home to endemics from the primary fish family Characidae. 

Molecular analyses based on an mtDNA cytochrome b molecular clock suggest that heroine cichlids (Martin and Bermingham 1998) colonized lower Mesoamerica approximately 18-15 million years ago (Smith and Bermingham 2005). Multiple lines of evidence suggest that the streams and rivers of lower Mesoamerica probably contained highly depauperate primary and secondary freshwater fish communities. The presence of empty ecological niches at the time of colonization probably fostered an adaptive radiation among the Cichlidae and Poeciliidae in order to fill the ‘ostariophysan vacuum’ that existed in Mesoamerica (Myers 1966; Bermingham and Martin 1998). This hypothesis explains the relatively high number of endemic cichlids and poeciliids in the San Juan ichthyofauna.

Other noteworthy fishes

Lake Nicaragua is well known for the bull shark (Carcharhinus leucas) and sawfish (Pristis pristis). Both fish are not restricted to freshwaters and have breeding populations at the mouth of the San Juan River. The tarpon (Megalops atlanticus) is sometimes found in the lake. The gar (Atractosteus tropicus) reaches its southern limit in the San Juan drainage.


Justification for delineation

Fish provinces from Bussing (1976) were revised and subdivided based on application of a similarity index to sub-basin fish presence/absence data.

Level of taxonomic exploration

The level of taxonomic exploration in the San Juan ecoregion is particularly good in the southern extent of the province, from and including the San Juan River to (and including) the Matina River drainage.


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