We examined fish assemblage structure in three headwater rain-forest streams in the Urubu River Basin, Central Amazonia, as it relates to habitat heterogeneity. Riffles and pools, two types of stream habitat, were defined by current, depth, and substrate parameters, adjusted for Amazonian stream characteristics. We assessed species richness, composition, and abundance as they varied between riffles and pools across three similar streams. Four riffles and four pools were identified in each stream and sampled four times during 1996 and 1997. The samples yielded a total of 856 individuals of 22 species. The most abundant species were in the families Characidae, Lebiasinidae, Helogenidae, and Rivulidae. We found an interactive influence of riffle/pool habitat and stream factors on species richness, composition, and abundance. Rain-forest stream fish assemblages are structured by both habitat and stream locality.