Abstract: The safety of the water environment in drinking water source areas is of vital importance to the lives and health of people, and is the top priority of ecological protection work. Delineations of drinking water source areas are mainly based on the analogue-empirical method, which cannot reflect the spatial and temporal distributions, or the compliance of water quality indicators in protection areas. In the study, the Environmental Fluid Dynamics Code (EFDC) was used to establish a two-dimensional vertical average model of the Baishi Reservoir. Its hydrodynamic and water environment change processes were simulated. The water age, eutrophication, and law of pollutant migration and attenuation were then analyzed to evaluate the rationality of the drinking water source protection areas as delineated by the analogue-empirical method. Through the verification of water level and storage capacity curves, and the verification of three typical annual water-level corresponding curves, R_RE < 0.1 and C_NSE > 0.85 . The simulation trend of the water quality simulation curve is consistent with the measured data, and the model is reliable. It is found that the average water ages in front of the dam are 304.4 d, 656.4 d, and 673.2 d, under the three typical annual conditions of high flow year, median flow year, and low flow year, respectively. The reservoir has long hydraulic exchange periods and is prone to eutrophication. The attenuation process of pollutants is simulated under the above three hydrodynamic conditions and the boundary conditions of the designed pollutants. The results demonstrate that the water quality of the water inlet is generally up to the standard, although the ammonia nitrogen in the high flow year exceeds the standard in the water inlet. The simulation results also show that the delineations of all water areas below the 116 m water level as the first-grade protection areas can meet the water quality requirements of the water intake. The delineation of drinking water source protection areas is therefore reasonable.