Habitat structure plays an important role in the structure and abundance of stream benthic assemblages. However, the implications of fine-scale flow variation associated with different substrate characteristics for the immigration and distribution of benthic animals are less clearly understood. The present study reports on the results of laboratory and field experiments in which substrate roughness was manipulated to generate micro-flow variation that in turn would affect benthic colonization. Measurements with an electric-current meter indicated the occurrence of turbulent flow with convex substrates, with its size and intensity being affected by substrate roughness. These will be considered in the light of habitat utilization by stream benthos.