A new in-stream model of phosphorus (P) and macrophyte dynamics, the Kennet Model, was applied to a reach of the River Kennet to investigate the impacts of changing flow conditions on macrophyte growth. The investigation was based on the assessment of two flow change scenarios, which both included the simulation of decreasing total phosphorus concentrations from a sewage treatment works due to improved effluent treatment. In the first scenario, the precipitation and potential evaporation outputs from a climate change model (HadCM2 GGx) where input into the catchment model INCA to predict the mean daily flows in the reach. In the second scenario, the mean daily flows observed in a historically dry year were repeated as input to the in-stream model to simulate an extended low flow period over 2 years. The simulation results suggest that changes in the seasonal distribution of flow were not detrimental to macrophyte growth. However, the simulation of extended periods of low flow suggests that a proliferation of epiphytic algae occurs, even when the in-stream phosphorus concentrations are reduced due to effluent treatment. This epiphytic growth was predicted to reduce the macrophyte peak biomass within the reach by approximately 80%. Thus, the model simulations suggest that flow was more important in controlling the macrophyte biomass in the River Kennet, than the in-stream phosphorus concentrations, which are elevated due to agricultural diffuse sources.