In rivers worldwide, hydrological persistence and variability (i.e. environmental stability) typically parallel longitudinal changes in habitat. This interaction complicates determination of the hierarchy of mechanisms that structure fish communities along rivers. In this study, we examined fish species richness and presence–absence in pools of an intermittent river system containing underground water storages (Fortescue River, north-west Australia), a system that was predicted to uncouple this relationship. Stability, measured by pool persistence, was unrelated to a pool's maximum depth or its position in the catchment, indicating partial decoupling. However, pool stability remained correlated with habitat diversity and log-transformed surface area. Model selection indicated that species richness was better described by pool stability and the landscape factor stream order than by within-pool habitat descriptors. Permanent pools low in the catchment contained more species than unstable pools in headwater streams. We conclude that the distribution of fish in the Fortescue River is shaped predominantly by processes of extirpation and re-colonisation. Management efforts in this river and similar intermittent systems should focus on the preservation of refuge pools, and limit the construction of barriers that limit dispersal.