An investigation was conducted to examine the influence of runoff input on the water quality of stratified reservoirs and to identify optimal artificial control strategies for positioning the intrusive layer, so as to enable the withdrawal of high-quality water. High-frequency and comprehensive in-situ monitoring of water quality indicators for spring snowmelt and summer storm runoff was conducted at Lijiahe reservoir (LJHR) in the northern foothills of the Qinling Mountains, to analyze the pollution characteristics, intrusive layer, and reservoir water quality response mechanisms. The results indicated that ① nitrogen/phosphorus (N/P) concentrations in runoff were significantly higher than those in baseflow, with snowmelt runoff was dominated by dissolved nutrients, while storm runoff contained dissolved N but particulate P. Moreover, N/P concentrations in storm runoff were significantly greater than those in snowmelt, which was attributed to differences in discharge. ② The effects of suspended solid (SS < kg/m³) on water density was neglected in the three runoffs events, and three different intrusive layers can be formed based on the differences between the runoff water temperature and the surface and bottom water temperatures of the reservoir. The water temperature of snowmelt runoff was typically higher than that of the reservoir bottom layer, leading to the development of overflows. Additionally, the abundance of available nutrients and the stable water environment during the early stages of reservoir stratification promoted rapid algal growth in the surface layer, which could easily induce algal blooms. ③ Prior to storm runoff inflow, the Water-lifting aerators system (WLAs) was used to regulate the intrusive layer of runoff seepage by modifying the vertical thermal structure of the reservoir. During the July torrential rain event, intermittent operation of the WLA resulted in higher water temperatures in the storm runoff [(18.46 ± 0.76)℃] compared to the bottom layer (16.67℃), leading to the formation of an interflow (837.9~815.6m). In September, continuous operation of the WLA raised the bottom water temperature to 19℃ before the storm inflow, which was higher than that of the incoming runoff [(12.35±0.59)℃], thereby inducing an underflow (800~828.2m). ④ Nutrient concentrations were significantly elevated in the intrusive layer, the formation of underflow induced by WLA placed the intrusive layer below the intake elevation (832m), effectively mitigating the impact of high-pollution-load runoff on water supply quality. Additionally, the compression of the intrusive layer reduces its thickness, thereby shortening the duration of its effects on water quality. This study provides a practical engineering reference for ensuring the safety of reservoir water supply. It is recommended activating the WLA at the early stages of reservoir stratification to inhibit algal blooms caused by snowmelt runoff and to increase the reservoir bottom water temperature above that of the runoff, thereby inducing the formation of underflow from runoff to achieve "high-quality mid-level water intake" during the storge period while ensuring "turbidity reduction and water clarity" during peak floods events.