Due to the continuous influence of human activities, phosphorus pollution in surface water has become a persistent problem that needs to be addressed since phosphorous entails certain risks and degrees of damage to ecosystems and humans. The presence and accumulation of total phosphorus (TP) concentrations in surface waters is the result of a combined effect of many natural and anthropogenic factors, and it is often difficult to intuitively identify the individual importance of each factor in regard to the pollution of the aquatic environment. Considering these issues, this study provides a new methodology to better understand the vulnerability of surface water to TP pollution and the factors that influence TP pollution through the application of two modeling approaches. This includes the boosted regression tree (BRT), an advanced machine learning method, and the traditional comprehensive index method (CIM). Different factors, such as natural variables (including slope, soil texture, normalized difference vegetation index (NDVI), precipitation, and drainage density) and point and nonpoint source anthropogenic factors were included to model the vulnerability of surface water to TP pollution. Two methods were used to produce a vulnerability map of surface water to TP pollution. Pearson correlation analysis was used to validate the two vulnerability assessment methods. The results showed that BRT was more strongly correlated than CIM. In addition, the importance ranking results showed that slope, precipitation, NDVI, decentralized livestock farming and soil texture had a greater influence on TP pollution. Industrial activities, scale livestock farming and population density, which are all contributing sources of pollution, were all relatively less important. The introduced methodology can be used to quickly identify the area most vulnerable to TP pollution and to develop problem specific adaptive policies and measures to reduce the damage from TP pollution.