Hydrology is an important driver of connectivity of fish stocks, and availability of habitat for feeding and reproduction. In the wet-dry tropics, unregulated rivers may flood in the wet season, creating floodplains for fish feeding and reproduction. During the dry season, many rivers cease to flow, and fish must survive in disconnected waterholes with diminishing resources. However, there has been little research on how these hydrological extremes in wet-dry tropical rivers affect fish production in comparison with other river systems. We measured fish biomass and condition in isolated perennial waterholes in the Flinders River catchment, Queensland throughout a dry season. We found that fish biomass decreased over the dry season as waterholes contracted, likely reflecting resource limitation and predation. The Flinders system had similar species composition to an arid zone river in central Australia, Cooper Creek. However, the key difference was that the arid zone river had more extreme ‘boom and bust’ periods of flow (and fish dynamics), while the Flinders system had more consistent inter-annual hydrological patterns. Fish in both systems are pre-adapted to these variable conditions so in both cases, there is a need to preserve natural flows to maintain fish productivity and diversity.