The dolphins Inia geoffrensis—boto and Sotalia fluviatilis—tucuxi are threatened cetaceans inhabiting river ecosystems in South America; population numbers are still lacking for many areas. This paper provides density and abundance estimations of boto and tucuxi in 15 rivers sampled during the past nine years as part of a multinational research alliance. Visual boat-survey data collection protocols and analyses have been developed since 2012 (based on Distance Sampling methods) and recently reviewed (2019) to improve robustness and comparability. Differences across the sampled rivers and the analyzed river basins (Amazon and Orinoco) pointed to a density/population size gradient with lower densities and abundances observed in the Orinoco basin (0.9–1.5 ind./km²), passing through the eastern Amazon basin (2–5 ind./km²), and the largest numbers found at the central Brazilian Amazon (lower Purus River—2012 (14.5 boto/km², N = 7672; 17.1 tucuxi/km², N = 9238)). However, in other parts of the central Amazon, the density of dolphins was smaller than expected for high productive whitewater rivers (1–1.7 ind./km² in the Japurá and Solimões rivers). We attributed these differences to specific features of the basin (e.g., hydro-geomorphology) as well as to the cumulative effects of anthropogenic activities.