A perceptible degradation in water quality complicates safe water supply for drinking and irrigation purposes. Therefore, this study aims at monitoring water quality changes and effective factors in the Dez River Basin, which are required to manage water resources effectively. To this end, the common influence of flow rate changes on water quality was separated by implementing seasonal Mann– Kendall test on residuals resulting from the LOWESS test. The results show that after adjusting the effects of seasonality and streamflow fluctuations, significant positive trends in most water quality parameters are still observed. It emphasizes the role of other factors controlling river water quality in the basin. Comparison of the trends of modified quality parameter time series (residuals) in different subbasins having natural or mad-made conditions, with or without significant groundwater resources, shows almost the same presented trends in water quality. This supports that, overall, minor changes occurred in land use, groundwater table, and environmental and human factors with no important influences on presented trends in water quality. Our analyses show that overall reduction in precipitation as well as positive trends in temperature and evaporation led to intensified streamflow variations, explaining the main changes in the river water quality of the basin.