Changes in the microdistribution of benthic macroinvertebrates were observed, between patches identified as refugia from high flow and the remaining benthic habitat, over a range of discharges in a small stream with prominent flow refugia. Total invertebrate abundances were similar across all patch types at baseflow, but local densities were higher in flow refugia after periods of high and fluctuating flow. Different species- and size-specific responses were observed: microdistributions of larval Chironomidae and small nymphs of the stonefly Leuctra nigra did not change with discharge. Conversely, the stonefly Nemurella pictetii and large nymphs of L. nigra were most abundant in refugia, relative to the remaining benthic habitat, during periods of high and fluctuating discharge. The interactive effects of leaf litter and local flow conditions on species microdistributions were investigated. In some seasons, some species may respond indirectly to hydraulic conditions through their direct response to litter mass. Observed microdistribution changes probably do not reflect very short-term reactions to individual flow events, but perhaps a longer-term response to seasonal flow conditions. These are some of the first field data implicating the role of in-stream flow refugia in macroinvertebrate community structure.