Fishes were sampled in riffle and pool habitats at 74 upland localities in the Little River system, southeastern Oklahoma and southwestern Arkansas, U.S.A. I asked how these two habitat-defined communities differed with regard to species abundance and incidence patterns, and how these differences varied along three environmental gradients: elevation, stream gradient, and stream size. Riffle and pool communities showed distinct and significant differences when ordinated in multivariate space defined by species abundance patterns. Sites with similar pool communities did not have similar riffle communities, and riffle and pool communities responded to environmental gradients in different ways. Elevation was the best predictor of pool community structure, whereas stream size was the best predictor of riffle communities. Overall, riffle habitats had fewer species than pool habitats and formed significant subsets of pool communities at 12 of 74 sites. I predicted that at small stream localities where riffles were unstable, riffle species would form subsets of the pool species communities, and both community types should show high similarities. The presence of faunal subsets was not associated with stream size, but faunal similarities were significantly higher at small stream localities. At the species level, 14 species were significantly associated with pool habitats, while only two were associated with riffle habitats. Riffle and pool communities, although linked by a continuous habitat gradient at the local scale, responded differently to large-scale environmental gradients. Local differences between these communities were predictable based on stream size.