River regulation and water extraction have impacted a range of ecosystem functions and processes in aquatic ecosystems. In the Murray Darling Basin, Australia, water reform aimed at restoring river and wetland ecosystems has resulted in significant increases in environmental flows. There is a limited understanding of how best to manage environmental flows to support productive and healthy food webs. Our objective was to explore the influence of different flow scenarios on the food web of Lachlan River, NSW, Australia. To do this we constructed a dynamic bioenergetic food web model using Ecopath with Ecosim. The model was parameterised with data long term monitoring data from the FLOW-MER research program. Using the fitted model we simulated scenarios that included with and without current environmental water allocations to see how changes in flow would influence the structure and productivity of the food web. Overall the results showed that simulations with more environmental water led to higher biomass for key fish species such as Murray Cod and Golden Perch. The simulations pointed to the importance of taxa such as decapods and Bony Bream as keystone groups in the food web. Whilst there are challenges in modelling food web interactions in systems with highly variable flow regimes, the approach highlights the importance using methods that integrate all trophic levels of the food the web and include both bottom-up and top-down interactions for assessing ecological responses to management interventions in river systems.