Taxonomic distinctness, a measure of diversity that captures the phylogenetic relatedness of an assemblage, has been successfully applied in several marine communities and appears to have considerable potential for environmental assessment and conservation. This approach has, however, not hitherto been used in structured freshwater systems. We evaluated this technique in the context of vulnerable tropical river drainages in India. We found that the inherent physical structure of river systems and longitudinal gradients in habitat characteristics influenced the pattern of taxonomic distinctness. Downstream locations were in general more taxonomically diverse than upstream ones. This in turn means that highly perturbed sites in the lower reaches of rivers would not display a reduction in taxonomic distinctness relative to a random expectation. The utility of the approach for detecting habitat and other disturbances on stream fish communities is thus limited. Implications of these unique properties of river ecosystems and their communities to conservation are discussed.