Abstract: Hybrid pumped-storage power stations, as clean energy facilities, are of great significance for achieving China’s “Dual Carbon” strategic goals. However, their daily pumping-generation cycles may disturb the existing aquatic ecological balance. In particular, water temperature impacts in environmentally sensitive water areas such as drinking water source protection zones require accurate assessment. Taking a hybrid pumped-storage power station in the upper reaches of the Qiantang River as a case study, this study constructs a vertical two-dimensional numerical water temperature model using CE-QUAL-W2 to simulate reservoir water temperature evolution in a typical dry year, predict the thermal stratification characteristics of the upper and lower reservoirs during operation, and quantitatively evaluate the effects of hybrid pumped-storage operation on reservoir water temperature structure. The hybrid pumped-storage project is located on a tributary of the upper reaches of the Qiantang River. Three hydraulic and hydropower projects, namely the upper reservoir, the lower reservoir and a water diversion project, have been built sequentially from upstream to downstream, alongside a hybrid pumped-storage power station currently under construction. Full-year daily meteorological and hydrological time series of a typical dry year (1985) in the watershed are adopted in this study, which are compiled from measured meteorological and hydrological data. Meteorological variables include air temperature, solar radiation, cloud cover, dew point temperature, wind speed, etc. The dew point temperature is calculated from local air temperature and relative humidity. Hydrological data consist of daily inflow discharge and water temperature, outflow discharge, and hourly pumping and generation flows of the hybrid pumped-storage station. The simulated outflow discharge and water temperature processes of the upper reservoir are used as the inflow boundary series for the lower reservoir. Combined with the hydrological characteristics of the watershed, May, August and December are selected as representative months for wet, normal and dry seasons, corresponding to the warming period, high-temperature period and cooling period, respectively. The contour plots of reservoir-wide water temperature distribution and monthly vertical water temperature profiles at typical cross-sections are adopted to analyze the thermal stratification characteristics of the upper and lower reservoirs after the operation of the hybrid pumped-storage station and assess its impacts on the baseline water temperature structure of the water source area. The results show that the operation of the hybrid pumped-storage station does not alter the fundamental thermal stratification pattern of the reservoirs. As a deep and large reservoir, the upper reservoir presents a five-layer vertical water temperature structure of “mixed layer–thermocline–hypolimnion–thermocline–hypolimnion” in high-temperature seasons and a three-layer structure of “mixed layer–thermocline–hypolimnion” in low-temperature seasons. Owing to its small storage capacity and shallow water depth, the lower reservoir exhibits weak thermal stratification with no distinct epilimnion and hypolimnion and small vertical temperature differences. The station operation induces slight local disturbances to the reservoir thermal structure. The upper pumping-generation intake is located near the upper layer of the reservoir; its pumping and generation processes impose limited disturbance on the thermocline around the intake during high-temperature seasons, accompanied by a slight increase in thermocline thickness. For the shallow lower reservoir, warmer inflow water in winter after station operation raises the vertical water temperature in front of the dam by approximately 0.5 ℃. After commissioning, the monthly trends of outflow water temperature from both reservoirs remain generally consistent with the baseline condition. The outflow water temperature rises slightly from June to December, with an overall temperature difference not exceeding 0.7 ℃. In general, the hybrid pumped-storage operation exerts minor impacts on the existing thermal stratification of the water source reservoirs. The studied river reach lies within the core zone of a national wetland park, which has high standards for biodiversity conservation and occupies an important ecological position. It is recommended that in situ water temperature monitoring be strengthened in the early operation stage of the power station, and real-time assessment of ecological effects induced by water temperature variations be carried out to support the optimization of eco-friendly reservoir operation and adaptive management schemes for the water source area.