Deep run-of-the-river reservoirs, like Xiluodu Reservoir, are characterized by large storage volumes and high flow rates. The thermodynamics and temperature distributions within these reservoirs are different from natural rivers and lakes. Research on Xiluodu Reservoir was conducted based on a series of long-term and high frequency thermistor chain data from November 2016 to September 2017. Annual heating and cooling periods were differentiated and the diurnal variations in surface water temperature as well as metalimnetic internal wave phenomena were analyzed. The surface heat flux was calculated using both observed data and a constructed numerical model to investigate its influence on the change in water temperature. Results revealed that the formation of the surface mixing layer is dominated by the total surface heat flux. Surface heat flux is an important factor when considering the increase of epilimnetic water temperature during the heating period. During the cooling period, the heat loss at the surface incites vertical mixing while inflow intrudes into the stratified volume, which together govern the cooling processes in the epilimnion. Results also revealed the formation of a metalimnetic internal wave with a period of 24 hours. This suggests that internal wave formation within Xiluodu Reservoir is related to dam hydropeaking. When comparing the surface heat flux calculated from measured meteorological data and that calculated by the numerical model with daily-averaged boundary conditions, the values from the numerical model tend to be smaller.