Heterogeneity in riverine habitats acts as a template for species evolution that influences river communities at different spatio-temporal scales. Although birds are conspicuous elements of these communities, the roles of phylogeny, functional traits and habitat character in their niche-use or species’ assembly have seldom been investigated. We explored these themes by surveying multiple headwaters over 3000 m of elevation in the Himalayan Mountains of India where specialist river birds reach their greatest diversity on Earth. After ordinating community composition, species traits and habitat character, we investigated whether river-bird traits varied with elevation in ways that were constrained or independent of phylogeny, hypothesising that trait patterns reflect environmental filtering. Community composition and trait representation varied strongly with elevation and river naturalness as species that foraged in the river/riparian ecotone gave way to small insectivores with obligate links to the river channel. These trends were influenced strongly by phylogeny as communities became more clustered by functional traits at higher elevation. Phylogenetic signals varied among traits, however, and were reflected in body mass, bill size and tarsus length more than in body size, tail length and breeding strategy. These variations imply that community assembly in high altitude river birds reflects a blend of phylogenetic constraint and habitat filtering coupled with some proximate niche-based moulding of trait character. We suggest that the regional co-existence of river birds in the Himalaya is facilitated by the same array of factors that together reflect the highly heterogeneous template of river habitats provided by these mountain headwaters.