The relationship between fisheries and climate has been given renewed emphasis owing to increasing concern regarding anthropogenically induced climate change. This relationship is particularly important for estuarine fisheries, where there are documented correlations between river discharge and productivity. The commercial catch of school prawns (Metapenaeus macleayi) has been shown to be positively correlated with the rates of river discharge in northern New South Wales, Australia. In the present study, a simulation model was developed to analyse the dynamics of the stock for 10 years under alternative river discharge scenarios, and the effectiveness of a series of management strategies under these scenarios was examined. A size-based metapopulation model was developed that incorporated the dynamics of school prawn populations in three habitats being harvested by three different fishing methods. The model indicated that both the growth and movement of prawns were affected by the rates of river discharge, and that higher rates of river discharge usually generated increased commercial catches, but this outcome was not certain. It was concluded that the population does not appear to be over exploited and that none of the three alternative management strategies performed better within the model than the current spatio-temporal closures, even under a wide range of river discharge scenarios.