The Rio Jauaperi forms the border between the states of Amazonas and Roraima in Brazil, flowing as a black-water tributary of the Rio Negro just south of the white-water Rio Branco. The river lies within the Lower Rio Branco-Jauaperi Extractive Reserve (Resex), a 581,173-hectare protected area established in June 2018 following two decades of advocacy by local communities. The river corridor also passes through or near other protected zones including the Baixo Rio Branco and Anauá National Forest, and approaches the indigenous territory of the Waimiri Atroari near its lower reaches.

A common put-in for guided expeditions is the bridge over the Jauaperi River in Roraima, approximately 440 km from Manaus — roughly seven hours by road. Paddlers typically travel downstream over 7 to 10 days, covering stretches of around 200 km before exiting via a 45 km dirt road (BR-431) to Comunidade Jundiá, then continuing approximately 351 km via BR-174 back to Manaus, with a total return drive of about six and a half hours. One early landmark is the Travessão waterfall, roughly 7 km from the starting point, notable for its rounded rock formations.

The river is characterized by extreme remoteness. Days can pass with only occasional local fishing boats in sight. Water color varies along the river from crystal clear to white to nearly black. The river supports more than 40 identified mammal species, ten of which appear on the IUCN endangered species list. Wildlife encounters can include giant otters, pink and tucuxi dolphins, manatees, howler monkeys, macaws, caimans, and piranha. The surrounding forest is primary Amazon rainforest with rich plant diversity.

Fewer than a thousand traditional inhabitants live along the river across approximately ten communities, subsisting on forest products and fishing. Commercial, ornamental, and sport fishing have been subject to legal restrictions, with a court injunction banning non-subsistence fishing in the area. Paddlers should be aware that mosquito presence is rated at maximum intensity. Internal combustion engines are prohibited in certain sections of the reserve, which contributes to the river's quiet character. Guided expeditions typically involve camping in hammocks and require a minimum group of two people.