Botos occur throughout the Amazon and Orinoco river basins, from the deltas upstream to where impassable rapids, waterfalls, lack of water, and possibly low temperatures block their movement (Best and da Silva 1989a,b). Three geographic populations have been recognized as subspecies: I. g. geoffrensis in the Amazon basin, except for the Madeira drainage in Bolivia above the Teotonio rapids, I. g. boliviensis in the upper Madeira drainage, and I. g. humboldltiana in the Orinoco basin (Rice 1998).

Besides the Amazon mainstem, I. g. geoffrensis has been recorded in the Tocantins (and das Mortes and Verde affluents), Xingu, Tapajós, Madeira (below the Teotonio rapids), Purus, Juruá, Ucayali, and Marañon (and Samiria affluent) tributaries flowing generally north, and in the Negro, Caqueta (Japurá), Apaporis, Putumayo, Napo, and Tigre tributaries flowing generally south (partial list from Best and da Silva 1989a,b; Leatherwood 1996).

In addition to the Madeira mainstem above the Teotonio rapids, I. g. boliviensis has been reported from the Beni (and Orton affluent), Iténez or Guaporé Basin (and Verde and Iporuporé affluents), and Mamoré Basin and its tributaries and afluents: Pirai, Grande, Ichilo, Chapare, Ibaré, Tijamuchi, Apere, Yacuma and Yata (Pilleri and Gihr 1977, Aliaga-Rossel et al. 2006, Aliaga-Rossel 2010).

In the Orinoco system, besides the mainstem, I. g. humboldtiana has been recorded in the Apuré (and Portuguesa and Guanmar affluents), Capanaparo, Cinaruco, Meta, Bita, Vichada, Tomo, Tuparro, Guaviare (and Guayabero affluent), Inírida, and Atabapo (and Temi affluent) tributaries flowing south and east, and in the Aro, Caura, Parquaza, Ventauri (San Juan affluent) tributaries flowing north and west, as well as in the Casiquiare Canal, which connects the Orinoco with the Negro River (a tributary of the Amazon), above and below the two sets of rapids at Puerto Ayacucho, which are the principal barriers that may (or may not) separate the Amazon and Orinoco populations (as summarized in Pilleri and Gihr 1977; Best and da Silva 1989a,b; Meade and Koehnken 1991). Botos have been seen crossing the first set of rapids at Puerto Ayacucho (Atures) during high water (Fernando Trujillo pers. comm. to B.D. Smith).