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Aim To determine the role of flow intermittence and species origin in shaping freshwater fish beta diversity across dryland riverscapes. Location Verde and Little Colorado River basins, United States. Methods Fish beta diversity was investigated in two large rivers with marked differences in basin-wide flow intermittence. Local site (continually flowing perennial vs. periodically flowing intermittent) and species (native vs. non-native) contributions to beta diversity were compared within each basin and over multiple decades (1987-2013) in relation to changing hydrologic conditions. Metacommunity dynamics were quantified using changes in alpha- (local), beta- and gamma- (regional) diversity through time. Results Beta-diversity patterns varied in relation to basin-wide intermittence. Intermittent sites were most influential to beta diversity where basin-wide intermittence was lower (Verde River), whereas perennial sites were most influential where basin-wide intermittence was higher (Little Colorado River). In intermittent sites, native fish species contributions to beta diversity tended to be higher than non-native species contributions. The relative contributions of perennial and intermittent sites to beta-diversity within each basin were invariant to annual flow regimes, whether atypically lower or higher than average flows, but somewhat related to intra-annual flow variation. Native species contributions to beta-diversity increased in years with high flow conditions in the Verde River. Over time, beta diversity decreased in the lower intermittence Verde River, indicating taxonomic homogenization, but remained relatively unchanged in the Little Colorado River. Main Conclusions Investigations of beta-diversity components over time are considered pivotal for conservation prioritization and planning. We found that both intermittent and perennial streams play complementary roles in supporting fish beta diversity, and that their relative contributions increase as basin wide availability of the habitat type decreases. Moreover, contributions of intermittent streams to overall beta diversity were relatively consistent through time and supported native fish diversity. Despite weakening policy protections of intermittent streams, these habitats are critical for supporting local species persistence and regional biodiversity.