A modelling study was undertaken to quantify effects that the climate likely to prevail in the 2050s might have on water quality in two contrasting UK rivers. In so doing, it pinpointed the extent to which time series of climate model output, for some variables derived following bias correction, are fit for purpose when used as a basis for projecting future water quality. Working at daily time step, the method involved linking regional climate model (HadRM3-PPE) projections, Future Flows Hydrology (rainfall-runoff modelling) and the QUESTOR river network water quality model. In the River Thames, the number of days when temperature, dissolved oxygen, biochemical oxygen demand and phytoplankton exceeded undesirable values (>25°C, <6 mg L −1 , >4 mg L −1 and >0.03 mg L −1 , respectively) was estimated to increase by 4.1-26.7 days per year. The changes do not reflect impacts of any possible change in land use or land management. In the River Ure, smaller increases in occurrence of undesirable water quality are likely to occur in the future (by 1.0-11.5 days per year) and some scenarios suggested no change. Results from 11 scenarios of the hydroclimatic inputs revealed considerable uncertainty around the levels of change, which prompted analysis of the sensitivity of the QUESTOR model to simulations of current climate and hydrology. Hydrological model errors were deemed of less significance than those associated with the derivation and downscaling of driving climatic variables (rainfall, air temperature and solar radiation). Errors associated with incomplete understanding of river water quality interactions with the aquatic ecosystem were found likely to be more substantial than those associated with hydrology, but less than those related to climate model inputs. These errors are largely a manifestation of uncertainty concerning the extent to which phytoplankton biomass is controlled by invertebrate grazers, particularly in mid-summer; and the degree to which this varies from year to year. The quality of data from climate models for generating flows and defining driving variables at the extremes of their distributions has been highlighted as the major source of uncertainty in water quality model outputs.