Flow regulation allowed flagellated and mucilaginous species to colonize the dammed areas. However, there was a noticeable reduction of phytoplankton diversity that persisted for more than 100 km after one of the dams. Functional turnover was low, suggesting that compositional changes occurred mainly among functionally similar species. We observed no effects of river damming on species dispersal. Furthermore, we assessed the effects of local environmental conditions on the phytoplankton taxonomic and functional composition using boosted regression trees (BRT). We used community-weighted means to test how the different traits were filtered by river damming. Functional diversity was estimated as the degree to which species within the same community differed from each other with respect to their trait composition (functional dispersion). Compositional changes were assessed by estimating the degree to which each community differed from all other communities within the regional pool (community distinctiveness) considering taxonomic and functional composition separately. Data were split at a reservoir level considering the sites within 30 km before and after each dam to analyze the effects of damming on the community composition. Phytoplankton samples were taken in 210 sites, spaced by 5 km, along the whole river channel. Furthermore, flow regulation allows species with different traits to colonize the increasingly lentic stretches resulting in higher functional diversity towards dams. We expect compositional changes to be higher at taxonomic than functional level especially in the dam-free stretches of the river because running waters select species able to cope with the water turbulence. Here we investigated the changes on the taxonomic and functional composition of the phytoplankton community in a large tropical dammed river. Although phytoplankton is a key biotic group to indicate changes in aquatic environments, the effects of river damming on the longitudinal distribution of phytoplankton communities are not widely addressed. River damming reduces the dispersal rates of biota and filter species by altering the local environmental conditions.