Potential increases of phytoplankton concentrations in river systems due to global warming and changing climate could pose a serious threat to the anthropogenic use of surface waters. Nevertheless, the extent of the effect of climatic alterations on phytoplankton concentrations in river systems has not yet been analysed in detail. In this study, we assess the impact of a change in precipitation and temperature on river phytoplankton concentration by means of a physically-based model. A scenario-neutral methodology has been employed to evaluate the effects of climate alterations on flow, phosphorus concentration and phytoplankton concentration of the River Thames (southern England). In particular, five groups of phytoplankton are considered, representing a range of size classes and pigment phenotypes, under three different land-use/land-management scenarios to assess their impact on phytoplankton population levels. The model results are evaluated within the framework of future climate projections, using the UK Climate Projections 09 (UKCP09) for the 2030s. The results of the model demonstrate that an increase in average phytoplankton concentration due to climate change is highly likely to occur, with the magnitude varying depending on the location along the River Thames. Cyanobacteria show significant increases under future climate change and land use change. An expansion of intensive agriculture accentuates the growth in phytoplankton, especially in the upper reaches of the River Thames. However, an optimal phosphorus removal mitigation strategy, which combines reduction of fertiliser application and phosphorus removal from wastewater, can help to reduce this increas