Non-point source pollution (NPSP) has become a critical pollution source after many improvements in point source pollution treatment have been made, particularly in China, due to intensive agricultural activities. Moreover, the impact of NPSP on surface water quality is significantly affected by extreme events, such as flooding. In this study, the soil and water assessment tool model was used to characterize the behaviours of NPSPs and to evaluate the effect of filter strips during flooding periods. The results showed that a flooding event in 2002 caused by a long duration of rainfall (event_1) contributed approximately 40 % of the annual sediment and organic N yield and 18.4 % of nitrate N yield. In 2007, more than 50 % of the annual sediment and organic N and 20 % of nitrate N export were caused by a flooding event due to heavy rainfall (event_2). The simulation results highlighted the severe threat of flooding events on aquatic environments. Furthermore, filter strips of different widths were simulated in these flooding scenarios to test their mitigation effects on the deterioration of surface water quality during these two events, and the 10-m filter strip did decrease more than 30-40 % of the loads of all NPSPs. Our study stresses that more attention should be paid to assessing the impact of flooding events on water quality management measures and pollution loads, as well as the effect of management practices on both aquatic and terrestrial ecosystems to develop sustainable water and soil resources.