To reduce the harm of water contamination incidents in drinking water source areas (DWSAs) and explore feasible approaches, the research developed a hydrodynamic water quality model for DWSAs based on two dimensional water quality and quantity equations, Geographic Information System (GIS), and Digital Elevation Model (DEM). The Heshangshan Drinking Water Source Area (HDWSA) in the Three Gorges Reservoir Area (TGRA) was selected as the research area, with total phosphorus (TP) as the representative pollutant in the water. The research investigated the changes in TP content during various hydrological phase under pollution incident, compared the duration and trends of TP concentration exceeding standard value before and after joint reservoir group dispatch. The results showed that the migration speed of TP pollutants varied from slowest to fastest in the following order: dry phase, recession phase, storage phase, and flood phase. Under pollution incident condition, the time demanded for TP content to meet standard value in each water phase was 36 min (dry phase), 33 min (recession phase), 30 min (storage phase), and 27 min (flood phase). The joint dispatch group 1–3 shortened the time required to meet standard value by 6–13 min (dry phase), 5–11 min (recession phase), 4–9 min (storage phase), and 3–7 min (flood phase). The trend of TP concentration before and after joint dispatch showed four stages: significant increase, sharp decrease, rapid decrease, and slow decrease. Joint dispatch of reservoir group can effectively reduced the TP concentration in DWSA under pollution incident.