This two-kilometer-wide belt that follows the north side of the river is part of the Río Indio-Maíz Biosphere Reserve, a 3,618-square-kilometer virgin rainforest, inaccessible to all but the most persistent scientists armed with a permit from the MARENA office in Managua.
The first access point to the Refugio is just six kilometers downstream of El Castillo [1] (or about three hours by boat from San Carlos). The western border of the reserve is made up by the Río Bartola at its confluence with the Río San Juan.
Arrange a hike through the local MARENA post, with AMEC in El Castillo, or at the ecolodge and research station, Refugio Bartola (tel. 505/8880-8754, refugiobartola [at] yahoo [dot] com, $50 pp with breakfast).
There are 11 rooms here on the corner of the protected area with wonderful views of the river. The compound and natural history museum is surrounded by rainforest and fueled by solar energy but is difficult to contact: You may need to wait until you’re in El Castillo.
Farther down the river you can access the Refugio de Vida Silvestre Río San Juan through any of the army posts including Boca San Carlos, Sarapiqui, and Delta.
Do not expect much more than a place to pitch your tent and friendly, if camouflaged, company.
Links:
[1] http://www.moon.com/destinations/nicaragua/rio-san-juan/down-the-rio-san-juan/el-castillo