Pumped-storage (PS) hydropower plants are expected to make an important contribution to energy storage in the next decades with growing market shares of new renewable electricity. PS operations affect the water quality of the connected water bodies by exchanging water between them but also by deep water withdrawal from the upper water body. Here, we assess the importance of these two processes in the context of recommissioning a PS hydropower plant by simulating different scenarios with the numerical hydrodynamic and water quality model CE-QUAL-W2. For extended PS operations, the results show significant impacts of the water exchange between the two water bodies on the seasonal dynamics of temperatures, stratification, nutrients, and ice cover, especially in the smaller upper reservoir. Deep water withdrawal was shown to strongly decrease the strength of summer stratification in the upper reservoir, shortening its duration by ~1.5 months, consequently improving oxygen availability, and reducing the accumulation of nutrients in the hypolimnion. These findings highlight the importance of assessing the effects of different options for water withdrawal depths in the design of PS hydropower plants, as well as the relevance of defining a reference state when a PS facility is to be recommissioned.