Robust relationships between biological characteristics and hydrological indices are required to provide a quantitative basis for environmental flows. Data from 1075 river sites distributed across New Zealand were used to investigate relationships between invertebrate communities and flow regimes, whilst also including the influence of additional environmental factors. Variance decomposition analysis was used to investigate the proportion of variance explained by hydrological, geomorphological, land cover, and catchment characteristics for the community matrix and each of three biotic indices representing taxon richness, Macroinvertebrate Community Index, and percentage of species in the Ephemeroptera, Plecoptera, and Trichoptera orders. Results showed that hydrological regime contributes a unique component to the explainable variation in the community, but this contribution is overestimated if other explanatory factors are not considered. A gradient forest model comprised of 93 random forest models, each predicting the probability of occurrence of a taxon, indicated the importance of high flows and also other dimensions of hydrological variation for predicting invertebrate taxa and biotic indices. Although many freshwater invertebrates in New Zealand are well adapted to a range of flow conditions through resistance traits and/or rapid colonization, this study suggests that several aspects of the flow regime influence invertebrate communities. These results suggest that environmental flows may be designed to sustain or even optimize specific ecological attributes or taxa, but changes along several dimensions of hydrological variability are likely to disadvantage other taxa and change invertebrate community composition.