In China, some areas with intensive agricultural use are facing serious environmental problems caused by non-point source pollution (NPSP) as a consequence of soil erosion (SE). Until now, simultaneous monitoring of NPSP and SE is difficult due to the intertwined effects of crop type, topography and management in these areas. In this study, we developed a new integrated method to simultaneously monitor SE and NPSP in an intensive agricultural area (about 6 000 km2) of Nanjing in eastern China, based on meteorological data, a geographic information system database and soil and water samples, and identified the main factors contributing to NPSP and SE by calculating the NPSP and SE loads in different sub-areas. The levels of soil total nitrogen (TN), total phosphorus (TP), available nitrogen (AN) and available phosphorus (AP) could be used to assess and predict the extent of NPSP and SE status in the study area. The most SE and NPSP loads occurred between April to August. The most seriously affected area in terms of SE and NPSP was the Jiangning District, implying that the effective management of SE and NPSP in this area should be considered as a priority. The sub-regions with higher vegetation coverage contributed to less SE and NPSP, confirming the conclusions of previous studies, namely that vegetation is an effective factor controlling SE and NPSP. Our quantitative method has both high precision and reliability for the simultaneous monitoring of SE and NPSP occurring in intensive agricultural areas.