Stream flow and associated seasonal hydrologic variation is a critical driver affecting the structure of aquatic macroinvertebrate communities. Quarterly aquatic macroinvertebrate sampling was carried out for a single year along the longitudinal axes of two streams in the southern Cape of South Africa. Stones-in-current, marginal vegetation, gravel-sand-mud, and stones-out-of-current biotopes were sampled for aquatic macroinvertebrates. Associations between macroinvertebrate communities and hydrographs were analyzed to investigate whether a non-perennial stream with greater flow variability had a higher prevalence of common or opportunistic species than a perennial one with less variable flow. Macroinvertebrate species richness was greater in the perennial as opposed to the non-perennial stream, where, on a seasonal basis, species richness increased from winter to autumn. Temporal species turnover differed between sites and streams, where reduced flows transformed the more dominant aquatic biotopes from stones-in-current into standing pools. Findings are that aquatic macroinvertebrates respond to changing flow conditions and reduced mean daily flows resulted in the disappearance of flow-dependant taxa and the arrival of non-flow-dependant taxa.