The impacts of changes in water temperature and flow on selected water quality parameters, as one of the consequences of climate change, were studied in river catchments in the Czech Republic with little anthropogenic influence. The impact of climate change was manifested by an increase in stream temperature by 1.15°C over 28 years. The selected water quality parameters were dependent on flow, with up to 10-fold increases in the concentrations of ammonia, phosphorus and chlorophyll-a at minimum flow levels. In river catchments with point source pollution predominating, significant pollution with ammonia nitrogen was observed. The influence of increased water temperature compared to flow rates was generally less marked and, with the exception of chlorophyll-a, rather positive. For existing land management and utilization of these river catchments, extreme changes in flow rates will influence the water quality more substantially than the water temperature itself.