Riverine fish living in unpredictable flow environments tend to be ecological generalists with traits that allow them to persist under highly variable and often harsh conditions associated with hydrological variation. Cooper Creek, an Australian dryland river, is characterised by extreme flow variability, especially in the magnitude, timing and duration of channel flows and floods, which, if they occur, do so mainly in summer. The present study examined the influence of hydrological variability on fish assemblages and abundance in four waterholes in the Windorah reach of Cooper Creek over eight occasions between 2001 and 2004. Antecedent flows had marked influences on fish species richness and assemblage structure. Following high summer flows, all waterholes supported a rich and abundant fish fauna, whereas fewer species and lower numbers were recorded following periods of zero channel flow. Recruitment of three of the four most common and abundant species was enhanced when intermittent flows inundated backwater and floodplain habitats that provide a food-rich environment. Opportunistic responses to rising channel flows and occasional large floods in Cooper Creek help to explain the prominent ‘boom’ patterns of fish production in this arid-zone river, whereas low-level recruitment during periods of low or no flow maintains populations of some species through the ‘bust’.