Background: Among the many types of lakes, the barrier lake attracts special attention. China’s Lake Jingpo is one of the world’s rare such alpine lakes. Spring freshet flooding and summer rainfall flooding are factors that significantly increase barrier lake instability while also impacting water quality. Results: This study constructed a hydrodynamic water-quality model to simulate the impacts of spring freshet flooding, summer rainfall flooding, and 30-year frequency rainfall flooding on the flow-field and water quality at Lake Jingpo. Results showed that the lake-area flow field was generally weak (mostly lower than 0.015 m/s), but spring freshet flooding in April and summer rainfall flooding in August-September increase flow velocities to 0.045 m/s and above, much higher than in other months. Mudanjiang is the largest river that enters Lake Jingpo. Its flow reaches 4.81×10 8 m 3 , 29.77×10 8 m 3 , and 58.4×10 8 m 3 during the spring freshet flooding, summer rainfall flooding and 30-year frequency rainfall flooding period, respectively. The longest diffusion distances were measured from the lake mouth to the point of impact; these were 16.3 km, 33.1km, and 43.6km for the above periods, respectively. Our research revealed that precipitation played an important role in seasonal water quality at Lake Jingpo, and larger amounts of precipitation, longer diffusion distances, and increased pollutant concentrations. Conclusions: Compared to the effects of the spring freshet flooding period, the summer rainfall flooding and 30-year frequency rainfall flooding period more significantly affected water quality at Lake Jingpo. There was more overall precipitation, longer diffusion distances, and increased pollutant concentrations in the lake area. Alpine barrier lake environments are very fragile, which need greater care efforts and more stringent measures to control pollution sources throughout entire catchment area.