The Rio Branco is a river with unique biogeographic and ecological features, threatened by the Brazilian Government’s plan to build a major hydroelectric dam and associated hydroway along its course. The river crosses one of Amazonia’s largest rainfall gradients and a major geomorphological boundary along a savanna/forest ecotone, marked by the Bem Querer rapids. Above the rapids, the upper Rio Branco runs through the Boa Vista sedimentary formation and crosses the crystalline rocks of the Guiana Shield, and its margins are flanked by gallery forests. Downriver, it runs through a low-lying sedimentary basin, with Amazonian floodplain forests along its margins. Here, we present the results of ∼ 15 years of ornithological research on the Branco and its major tributaries, providing baseline data and evaluating potential threats to the riverine avifauna. Our surveys included opportunistic observations and standardized surveys along the entire length of the river in 16 systematically distributed localities. We catalogued 439 bird species, 87% of which are documented by physical evidence (specimens, recordings, photographs). Forty-six percent are restricted to single habitats, suggesting a high degree of habitat specialisation. A third of the species are widely distributed along the river, whereas 45% are restricted to either the upper or the lower Rio Branco, including 40 and 30 Indicator Species, respectively. Twenty-five species are threatened at global or national levels, including two ‘Critically Endangered’, nine ‘Vulnerable’, and 14 ‘Near Threatened’. We present a list of 50 bird species that are candidates for monitoring studies. Threats to the avifauna from dam construction include permanent flooding above the dam, eliminating gallery forests, river islands, and sandy beaches, and the disruption of the flood pulse along the river, affecting river island and floodplain forest specialists, many of which are globally threatened with extinction. If built, the Bem Querer dam will wipe out the ecotone region and affect dramatically the river’s avifauna.