Hydrogeological evolution and three-dimensional numerical modeling were investigated in an urban area of Beijing. The main conclusion illustrate that hydrogeochemical modeling, geological statistics and spatial analysis on GIS can be applied to jude and measure the anthropogenic influence on the chemical composition of groundwater, as was assessment of stable isotope ratios approach in combination with chemical and hydrogeological data revealed that wastewater is the prevailing source of nitrogen. Moreover investigations using laboratory columns and field observations revealed that clay controls the concentration of cations, silica, and chloride ions in groundwater, indicating that clay layer is an important factor involved in control of groundwater quality. Then MODFLOW model was able to represent the negative impacts caused by excessive extraction of groundwater. PHT3D model was also able to quantify the influence of various land use functions on groundwater quality and deduce geochemical processes occurring in the aquifers. Finally, a novel conceptual model for an urban area that can be used in the future to evaluate site remediation scenarios was developed as part of this work.