Groundwater with relatively stable quantity and quality is commonly used by human being. However, as the over-mining of groundwater, problems such as groundwater funnel, land subsidence and salt water intrusion have emerged. In order to avoid further deterioration of hydrogeological problems in over-mining regions, it is necessary to conduct the assessment of groundwater risk. In this paper, risks of shallow and deep groundwater in the water intake area of the South-to-North Water Transfer Project in Tianjin, China, were evaluated. Firstly, two sets of four-level evaluation index system were constructed based on the different characteristics of shallow and deep groundwater. Secondly, based on the normalized factor values and the synthetic weights, the risk values of shallow and deep groundwater were calculated. Lastly, the uncertainty of groundwater risk assessment was analyzed by indicator kriging method. The results meet the decision maker's demand for risk information, and overcome previous risk assessment results expressed in the form of deterministic point estimations, which ignore the uncertainty of risk assessment.