Water source reservoir is the most important drinking water source for urban residents. Although the water quality of newly built reservoir is generally good, the water quality of reservoir is constantly changing due to the common influence of rainfall runoff into storage, hydrodynamic conditions and stratified structure changes during reservoir impoundment. This study focuses on exploring the law of water quality change in the process of reservoir storage and analyzing the pollution characteristics of water source reservoir. The water quality in the upstream channel and reservoir area of Sanhekou Reservoir in Hanzhong City, Shaanxi Province was tracked and monitored by the method of fixed frequency sampling, and the influence of the upstream water quality, the stratification structure of the reservoir water and the change of hydrodynamic conditions on the water quality of the reservoir was analyzed. The results show that ：(1)the first large discharge water storage process in Sanhekou from June to July 2021 is affected by the influent temperature, and the incoming water enters the reservoir in the form of undercurrent and forms a new temperature stratification at the bottom. The formation of the double thermocline structure leads to the formation of anaerobic water layers with a thickness of 15 and 10 m in the middle and bottom of the water body respectively. (2)In early September, the second large runoff into the reservoir completely destroyed the thermal stratification structure of the water body, and the water body realized complete mixing under the combined action of runoff and air temperature.(3) The water quality of the water source reservoir during the storage process is affected by the inflow runoff and the stratified structure of the water body: From June to August, the runoff of the reservoir was small and the pollution load was low, the concentration of nitrogen, phosphorus and organic matter in the reservoir area fluctuated slightly, and the thermal stratification structure hindered the vertical transfer of pollutants, so that the total nitrogen concentration and permananate index of the thermocline water showed large vertical values, 1.78mg/L and 6.0mg/L, respectively. From August to early September, the runoff of the reservoir was large and the pollution load was high. The concentration of nitrogen, phosphorus and organic pollutants in the whole reservoir increased significantly, with the concentration of total nitrogen increasing from 1.07 mg/L to 1.56 mg/L, and the concentration of total phosphorus increasing from 0.021 mg/L to 0.029 mg/L. The average permanganate index increased from 5.18 mg/L to 6.18 mg/L. In the process of reservoir storage, upstream runoff into the reservoir is an important factor affecting the stratified structure of the reservoir water and the concentration of pollutants.