Ecosystem based fisheries management (EBFM) has gained considerable attention in marine systems over the last decade, including the use of ecosystem models to understand how changes in food-webs affect higher trophic levels. The use of quantitative ecosystem models to manage freshwater fisheries has lagged by comparison, despite well entrenched concepts linking seasonal flood pulses to primary and secondary production, with flow on effects for higher order consumers. This talk will contrast the application of ecosystem models in marine and freshwater environments, and demonstrate the application of ecosystem modelling to examine the impacts of flow management and food-web changes on fish production in the southern Murray-Darling Basin. This case study highlights a number of critical knowledge gaps but also provides valuable insights on the potential complementary roles that different management actions will likely have in restoring native fish abundances.