Abstract: Marine water quality is of importance to the health of the bay ecosystem. For improving the water quality, the total pollutant discharge control of sea areas based on the environmental capacity is the primary means. In this paper, under the water quality requirements and the nonlinear relationship between pollution sources and environmental capacity, the impact of pollution sources discharging into Xincun lagoon was studied. The combination of random forest algorithm and the conventional water quality model was employed in the analysis process. The results showed that among the 41 pollution sources from three categories, i.e., fishing raft culture, urban sewage and river runoff, 10 pollution sources had an overall impact on inorganic nitrogen and phosphate environmental capacity. Among the three categories, fishing raft culture is the main one affecting the inorganic nitrogen environmental capacity. However, in terms of the phosphate environmental capacity, the impact from three types of pollution sources makes a slight difference.