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Climate extremes, in particular droughts, are significant driving forces towards riverine ecosystem disturbance. Drought impacts on stream ecosystems include losses that can be either direct (e.g., destruction of habitat for aquatic species) or indirect (e.g., deterioration of water quality, soil quality, and increased chance of wildfires). This paper combines hydrologic drought and water quality changes during droughts and represents a multistage framework to detect and characterize hydrological droughts while considering water quality parameters. This method is applied to 52 streamflow stations in the state of California, USA, over the study period of 1950-2010. The framework is assessed and validated based on two drought events declared by the state in 2002 and 2008. Results show that there are two opposite drought propagation patterns in northern and southern California. In general, northern California indicates more frequent droughts with shorter time to recover. Chronology of drought shows that stations located in southern California have not followed a specific pattern but they experienced longer drought episodes with prolonged drought recovery. When considering water quality, results show that droughts either deteriorate or enhance water systems, depending on the parameter of interest. Undesirable changes (e.g., increased temperature and decreased dissolved oxygen) are observed during droughts. In contrast, decreased turbidity is detected in rivers during drought episodes, which is desirable in water systems. Nevertheless, water quality deteriorates during drought recovery, even after drought termination. Depending on climatic and streamflow characteristics of the watersheds, it was found that it would take nearly 2 months on average for water quality to recover after drought termination.