Abstract – The salmonid Oncorhynchus mykiss tends to inhabit forested or snow-fed streams having cold reliable flows, but in the California chaparral they inhabit rain-fed stream networks with extensive areas of intermittent flow. We hypothesised that hydrological mechanisms in such watersheds tend to spatially segregate spawning and over-summering habitats, and tested the hypothesis using observations from a series of tributaries in a pristine watershed. Consistent with the hypothesis, reaches with suitably sized spawning gravels tended to occur in intermittent tributaries, and also the perennial mainstem (which was too warm for over-summering). In early summer, juvenile O. mykiss (<10 cm) occurred at similar densities in the intermittent and perennial tributaries, but larger fish had greater densities in perennial tributaries. Large wood debris would be expected to mitigate the spatial segregation of habitats somewhat, but was scarce, though stream-side outcrops appeared to partially compensate by forcing gravel bars in high-gradient channels.