Most of our current understanding of rarity has come from studies of terrestrial plants and animals, whereas freshwater habitats remain poorly documented under this topic. Here we considered the spatial distribution patterns of rarity at the river catchment scale, for five freshwater taxa (fish, Ephemeroptera, Plecoptera, Trichoptera and Coleoptera) in southwestern France. The data were collected at 554 and 155 sampling sites for fish and aquatic insects, respectively. General Linear Modelling was used to assess the influence of some typological variables (elevation, stream order, distance from source, and reach slope) on local numbers of rare species (restricted range). The relative numbers of rare species per taxa varied from 16% (Plecoptera) to 59% (Trichoptera). GLM chiefly yielded highly significant correlations between rarity and distance from the source and/or elevation for all taxa, showing that numbers of rare stream species increase towards downstream areas within the stream system. The spatial patterns in rarity for the different study taxa were rather concordant, probably as a result of similar responses to environmental conditions. By focusing on integrative variables, we emphasized the influence of river typology on the rarity of aquatic animals. Areas which carry rare species may concentrate an important fraction of the regional biodiversity. If end-users need geographic models (i.e. maps) to design river management frameworks, numerical patterning is needed to provide theoretical backgrounds: by predicting what the rarity should be like in a given area, we can provide explicit spatial schemes that may be useful to target further research, and to implement management options.