1. Temporary streams comprise a large proportion of the total length of most stream networks, and the great majority of arid-land stream networks, so it is important to understand their contribution to biotic diversity at both local and landscape scales.
2. In late winter 2010, we sampled invertebrate assemblages in 12 reaches of a large arid-land stream network (including perennial and intermittent headwaters, intermittent middle reaches and perennial rivers) in south-east Arizona, U.S.A. Intermittent reaches had then been flowing for c. 60 days, following a dry period of more than 450 days. We sampled a subset of the perennial study reaches three more times between 2009 and 2011. Since intermittent reaches were dry during these additional sampling periods, we used assemblage data from two other intermittent streams in the study network (sampled in 2004–05 and 2010) to explore interannual variability in intermittent stream assemblage composition.
3. Invertebrate richness was lowest in intermittent reaches, despite their often being connected to species-rich perennial reaches. The assemblages of these intermittent reaches were not simply a subset of the species in perennial streams, but rather were dominated by a suite of stoneflies, blackflies and midges with adaptations to intermittency (e.g. egg and/or larval diapause). On average, 86% of individuals in these samples were specialists or exclusive to intermittent streams. Predators were 7–14 times more abundant in perennial than in intermittent reaches.
4. Despite being separated by long distances (12–25 km) and having very different physical characteristics, the assemblages of perennial headwaters and rivers were more similar to one another than to intervening intermittent reaches, emphasising the prime importance of local hydrology in this system.
5. The duration and recurrence intervals of dry periods, and the relative importance of dispersal from perennial refuges, probably influence the magnitude of biological differences between neighbouring perennial and temporary streams. Although perennial headwaters supported the highest diversity of invertebrates, intermittent reaches supported a number of unique or locally rare species and as such contribute to regional species diversity and should be included in conservation planning.