The sustainable productivity of estuarine fisheries worldwide is threatened by over-fishing, habitat destruction and water impoundment. In some cases, the natural variability of freshwater inputs has been shown to affect catch when low flows reduce nutrient input and inundated nursery habitats. Historically, the annual commercial catch of barramundi (Lates calcarifer) in Queensland has been highly variable for reasons not fully understood. In conjunction with a life-cycle model, statistical analyses of climate variables and barramundi catch data from the Princess Charlotte Bay area identified several significant relationships. Warm sea surface temperatures, high rainfall, increased freshwater flow and low evaporation (all measures of an extensive and productive nursery habitat) were significantly correlated with barramundi catch 2 years later and suggest that young barramundi survival is enhanced under these conditions. Catchability was significantly increased with high freshwater flow and rainfall events in the year of catch. A forward stepwise ridge regression model that included a measure of rainfall and evaporation 2 years before catch explained 62% of the variance in catch adjusted for effort. It is recommended that the impact of climate variability be considered in the management of wild barramundi stocks and possibly other species not yet examined.