Modification of freshwater flow regimes can impact estuarine ecosystems at the receiving end of these flows. This is particularly true in tropical areas, such as the wet-dry tropics, where major freshwater flows in the wet season may result in prolonged and large-scale flooding, followed by periods of little or no flow during an extended dry season. Estuarine species, such as the commercially important prawn Penaeus merguiensis, have lifecycles adapted to seasonal flows. The potential effects of flow regulation on estimated catches of P. merguiensis were explored using a Bayesian belief network (BBN) model. Probability statements were generated about the ecological implications of different magnitudes of natural flow, as well as three water-extraction scenarios: 1) reduced flow in the wet season; 2) the introduction of flow in the dry season; and 3) the combination of scenario one and two. Thresholds of freshwater flow that affect the likelihood of high prawn catches in the fishery were identified, and the cumulative effects explored. This is the first time that these thresholds have been identified and the model suggests there is little capacity to regulate or modify the freshwater flow without reducing the probability of high prawn catches.