The Mediterranean region is a climate change hotspot, especially concerning issues of hydrological planning and urban water supply systems. In this context, the Jucar River Basin (Spain) presents an increase of frequency, intensity and duration of extreme meteorological phenomena, such as torrential rains, droughts or heat waves, which directly affect the quantity and quality of raw water available for drinking. This paper aims to analyze the effects of climate change on the raw water quality of the Jucar River Basin District, which mainly supplies the city of Valencia and its metropolitan area, in order to adapt drinking water treatments to new conditions and opportunities. For this purpose, we used observed data of water quality parameters from four stations and climate drivers from seven Earth system models of the latest Coupled Model Intercomparison Project—Phase 6. To model water quality (turbidity and conductivity) in the past and future scenarios, this study employs a backward stepwise regression taking into account daily values of mean temperature, maximum temperature, total rainfall and minimum and maximum relative humidity. Results showed that the model performance of the water quality simulation is more adequate for short moving-average windows (about 2–7 days) for turbidity and longer windows (about 30–60 days) for conductivity. Concerning the future scenarios, the most significant change was found in the projected increase of conductivity for the station of the Júcar river, between 4 and 11% by 2100, respectively, under the medium (SSP2–4.5) and pessimistic (SSP5–8.5) emission scenarios. The joint use of these types of management and monitoring tools may help the managers in charge of carrying out the different water treatments needed to apply a better plan to raw water and may help them identify future threats and investment needs to adapt the urban water supply systems to the changing conditions of raw water, such as turbidity or conductivity, as a consequence of climate change.