Extreme weather has recently become frequent. Heavy rainfall forms storm runoff, which is usually very turbid and contains a high concentration of organic matter, therefore affecting water quality when it enters reservoirs. The large canyon-shaped Heihe Reservoir is the most important raw water source for the city of Xi'an. During the flood season, storm runoff flows into the reservoir as a density current. We determined the relationship among inflow peak discharge (Q), suspended sediment concentration, inflow water temperature, and undercurrent water density. The relationships between (Q) and inflow suspended sediment concentration (C S0 ) could be described by the equation C S0 = 0.3899 × e 0.0025Q , that between C S0 and suspended sediment concentration at the entrance of the main reservoir area S1 (C S1 ) was determined using C S1 = 0.0346 × e 0.2335CS0 , and air temperature (T a ) and inflow water temperature (T w ) based on the meteorological data were related as follows: T w = 0.7718 × T a + 1.0979. Then, we calculated the density of the undercurrent layer. Compared to the vertical water density distribution at S1 before rainfall, the undercurrent elevation was determined based on the principle of equivalent density inflow. Based on our results, we proposed schemes for optimizing water intake selection and flood discharge during the flood season.