Aquatic invertebrates were collected from perennial and intermittent sites along the Selwyn River, a New Zealand intermittent-perennial river. Sixteen sites were visited monthly between 2003-04 to collect quantitative invertebrate samples and measure discharge, water velocity and depth, water chemistry, substrate composition, and chlorophyll a biomass. Discharge measurements were used to calibrate a hydrologic model that predicted historic flow conditions at each site. From the hydrologic model, we extracted site-specific estimates of the duration of flow, average frequency of drying, 7-day average discharge prior to sampling, and days since flooding (> 3x median discharge), among other hydrological statistics. Invertebrate density and richness were significantly higher at perennial sites compared to intermittent sites. Average EPT richness and density were significantly correlated with the modeled estimate of the long-term average flow duration at each site (r² = 0.55 and 0.32, respectively). However, Diptera richness and density did not correlate with any modeled estimate of flow duration or drying frequency. Direct gradient ordination (DCA) revealed that primary differences in invertebrate composition among sites were best explained by the long-term average flow-duration and frequency of drying. Further analyses indicated that invertebrate assemblages at intermittent sites were nested subsets of the taxa at perennial sites.