For the many lakes world-wide with short residence times, changes to the rate of water throughput may have important effects on lake ecology. We studied relationships between current and predicted residence times and phytoplankton biomass using a eutrophic lake in the north-west of England with an annual residence time averaging about 20 days, as a test case. Using 32 years of recent hydrological flow data for Bassenthwaite Lake, multiple sets of scaled flow for each year, and the process-based phytoplankton response model, PROTECH, we modelled the effects of changing river flow on phytoplankton biomass in the lake. The impact on biomass was shown to depend on seasonal changes in flow rather than annual changes. Furthermore, there was a qualitative difference in impact depending on whether the nutrient loading to the lake came principally from flow-independent sources, or from flow-dependent ones. Predictions for changes in river flow under future climate scenarios in the north-west of England have suggested that, despite little change in the annual flow magnitude, there will be a shift to greater flow in the winter and lesser flow in the summer. Applying these flow predictions to our modelling of Bassenthwaite Lake revealed that, with flow-independent nutrient loading, and no overall increase in nutrient load, phytoplankton abundance in the summer could increase by up to 70%, including an increased proportion of Cyanobacteria. Conversely, were the loading completely dependent on the flow, the biomass would fall. In many parts of the world, river flow is expected to decrease in the summer even more than in England, suggesting these areas may expect substantial changes to seasonal phytoplankton biomass as a result of climate-driven changes to seasonal river flow. Such changes would be in addition to any other changes owing to warming effects or eutrophication.