Understanding the drivers of stream macroinvertebrate distribution patterns—the most diverse animal group in freshwater ecosystems—is a major goal in freshwater biogeography. Climate and topography have been shown to explain species’ distributions at continental scales, but the contribution of natural and anthropogenically altered streamflow is often omitted in large‐scale analyses due to the lack of appropriate data. We test how macroinvertebrate occurrences can be linked to streamflow observations and evaluate the relative importance of streamflow regimes and water use for macroinvertebrate occurrences from 19 orders across Europe. We first paired species sampling locations with hydrological gauging stations considering 5 combinations of the geographic distance and difference in flow accumulation (upstream contributing area). We then used Generalized Linear Models to assess the influence of the streamflow regime, simulated water use, and climate and topography on the occurrence of macroinvertebrates. The pairing method that assigned species records to the closest gauging station in terms of both distance and flow accumulation performed best. Most of the species studied occurred preferentially in river habitats with low mean annual streamflow and streamflow variability, high winter streamflow, and low levels of water withdrawals for irrigation or manufacturing. We conclude that flow accumulation is a useful proxy to evaluate the proximity of species records to gauging stations, omitting species records that do not belong to a given stream reach. The strong contribution of streamflow and water use indicators on macroinvertebrate occurrences underline their importance for yielding robust occurrence estimates.