Physicochemical conditions in refugia must remain within the tolerance limits of aquatic invertebrates if they are to persist in intermittent streams when surface water is absent. We investigated shallow streambed sediments as a refuge for aquatic invertebrates and survival of invertebrates at high temperatures during the dry period in 3 headwater intermittent streams in New Zealand. Sediments from dry stream beds inundated in the laboratory contained 37 of the 53 taxa found in nearby flowing streams, a result suggesting that many taxa attempt to use the dry stream bed as a refuge during dry periods. Relative abundances of microcrustacea (copepods and ostracods), Gastropoda and Coleoptera (mostly Scirtidae) were greater in rewetted sediments than in sediments from nearby flowing streams, and several Ephemeroptera, Plecoptera, and Trichoptera taxa were present in low densities in rewetted sediments. All taxa that became active in rewetted sediments, except Hydrobiosidae, Tarapsyche olis (Trichoptera), Lymnaea (Gastropoda), Chironomini, and Cladocera, were active within a few hours of rewetting. We tested invertebrate survival in rewetted sediments at high temperatures (comparable to near-surface temperatures of dry stream beds in the field) in 2 experiments. In experiment 1, abundances of all major taxa were 11 to 94% lower in warm (air temperature  =  30°C, sediment temperatures  =  22–25°C for 1 h/d) than in cooler treatments. In experiment 2, abundances of most major taxa except Coleoptera and Acari were >75% lower in warm (air temperature  =  37°C, sediment temperature  =  32°C for 1 h/d) than in cooler treatments. Mid-summer daily maximum temperatures in the top 5 cm of the stream bed were 35 to 42°C in open pasture, 17 to 19°C under dense forest canopy, and 22 to 29°C under sparse riparian trees. Results suggest that maintaining the microclimate provided by riparian forest is important for protecting the aquatic invertebrate community in intermittent streams.