The water temperature structure of the reservoir is not only critical for the downstream water temperature and the ecological environment, but also serves as an essential boundary condition for the dam temperature field, particularly impacting the stress and deformation of high arch dams. Focusing on the Baihetan Arch Dam, this study employs long-term monitoring data to reveal the distribution patterns and influencing factors of the reservoir water temperature during the impoundment and initial operation phases of the arch dam. It is concluded that the water temperature within the Baihetan Reservoir exhibits a distinct stratified pattern that varies with elevation and manifests a pronounced annual cycle. This stratification initiates in the spring, intensifies during the summer and autumn months, and gradually dissipates as winter approaches. Fluctuations in the air temperature and the process of impoundment are identified as pivotal factors driving the thermal stratification of the reservoir. This research provides a scientific basis for the ecological protection of the Baihetan Reservoir and the analysis of the dam’s operational state.