Tropical savannah river systems have distinct and predictable flow seasonality; but vary in dry season permanency and wet season flow-pulse characteristics. Understanding how flow permanence and variability influence fish assemblages, and their utility in predicting future change, are key knowledge gaps that impede effective management of these systems. We examined the influence of flow variability on the structure and diversity of freshwater fish assemblages across rivers of the Northern Territory, Australia. Despite a common species pool, distinct assemblages emerged that varied predictably across three hydrological river types: Intermittent, Perennial Stable and Perennial Flashy flow regimes. Species richness was greatest in rivers with Perennial Stable flows, and beta-diversity was greatest in Intermittent rivers. Life history strategy was a poor predictor of species abundances within hydrological river type. The distinct fish assemblages evident among hydrological types may provide some cautious ability to forecast fish assemblage changes with future hydrological changes (e.g. if perennial streams became more flashy or intermittent), and also to predict fish assemblages expected in unsampled rivers. Our findings support the importance of maintaining regional flow-habitat heterogeneity and connectivity between hydrological river types, and their essential role in conserving tropical freshwater fish diversity into an uncertain hydrological future.