Fisheries and natural water resources across the world are under increasing pressure from human activity, including fishing and irrigated agriculture. There is an urgent need for information on the climatic/hydrologic drivers of fishery productivity that can be readily applied to management. We use a generalized linear mixed model framework of catch curve regression to resolve the key climatic/hydrological drivers of recruitment in Barramundi Lates calcarifer using biochronological (otolith aging) data collected from four river-estuary systems in the Northern Territory, Australia. These models were then used to generate estimates of the year class strength (YCS) outcomes of different water abstraction scenarios (ranging from 10% to 40% abstraction per season/annum) for two of the rivers in low, moderate, and high discharge years. Barramundi YCS displayed strong interannual variation and was positively correlated with regional monsoon activity in all four rivers. River-specific analyses identified strong relationships between YCS and several river-specific hydrology variables, including wet and dry season discharge and flow duration. Water abstraction scenario models based on YCS–hydrology relationships predicted reductions of >30% in YCS in several cases, suggesting that increased water resource development in the future may pose risks for Barramundi recruitment and fishery productivity. Our study demonstrates the importance of the tropical monsoon as a driver of Barramundi recruitment and the potential for detrimental impacts of increased water abstraction on fishery productivity. The biochronological and statistical approaches we used have the potential to be broadly applied to inform policy and management of water resource and fisheries.