Dryland rivers in arid and semi-arid regions drain approximately one-third of the Earth's land area, yet basic aspects of their ecology are poorly documented and many are threatened by excessive water use leading to alterations of the flow regime. Management of dryland rivers imperilled by changes to the flow regime requires quantitative hydro-ecological relationships and models to support environmental flow restoration strategies and to define ecological response indicators for assessment of trends in ecological health. Fish living in dryland rivers experience highly variable levels of food resources associated with 'boom and bust' productivity patterns driven by highly irregular episodes of rainfall, runoff and floodplain inundation followed by busts associated with drying of remnant aquatic habitats. To cope with variable food resource levels, fish store energy as fat during productivity booms, enabling them to breed later or to survive through extended periods of limited food resources. This study tracked temporal patterns of body condition and recruitment success of the four most abundant fish species in two Australian dryland river systems with contrasting patterns of flow variability, Cooper Creek and the Moonie River. We found consistent responses to flow magnitude and timing for body condition and/or recruitment success in Cooper Creek but fewer responses in the Moonie River. Results suggest that the fish metrics and relationships to flow established for Cooper Creek may apply in similar dryland rivers exhibiting clear boom and bust patterns, whereas the Moonie River results could be applicable to rivers with less variable flow patterns and fewer spells of zero flows. Our study demonstrates that simple, non-destructive methods based on fish length and weight provide useful biological indicators of response to flow variability provided that care is taken with species selection and that hydro-ecological relationships are calibrated for each contrasting type of hydrologic regime.