Vulnerability of water environmental is defined as a measure of the degree of water pollution and its susceptibility and resilience under the influence of both human activities and natural causes. Analysis in this study indicates that water environment in a humid and intensive human activity area such as Southern China is more vulnerable to water quality than to water quantity. The vulnerability of water environment is the key element of water security in these regions. This study provided a new approach to quantify the vulnerability of surface water environment in humid areas through a case study in Southern China. Taking the pollution of water environment as an input-output process, the classic Data Envelopment Analysis method (DEA) which has often been used in the management science, was introduced to establish an evaluation model to access the vulnerability of surface water environment. The analysis results for the 7 water resources districts in the Pearl River Basin of China using the SEA method showed that majority of these water resources districts have abundant water resources, greater carrying capacity, and less vulnerable to shortage of water resources and contamination of water environment.