Karst groundwater flow processes is difficult to estimate due to heterogeneity of aqueous media. This paper, taken Fangshan, the southeast of Beijing, as the research area. In order to improve the understanding of groundwater evolution in Fangshan karst groundwatre system, hydrochemical and isotopic data were sampled in the Xiayunling-Longmentai synclinorium hydrogeological unit and analysed as indicators for conceptual model to identify the origins of groundwater, hydrogeochemical evolution and the geological structure effects. The results show that: groundwater mainly originates from the local rainfall, hydrochemical types of which are mainly HCO3-Ca·Mg and almost unchanged with time. The origin of primary chemical components is associated with dissolution and precipitation of aquifer minerals, including calcium carbonate, dolomite, and gypsum. From the northwest and northeast mountain regions to the piedmont zone in the southeast, δ18O and δD of groundwater generally showed an increasing trend. For the hydrochemical origin, the mineral composition of groundwater should be accumulated from the mounrain to piedmont region. The geological structure could control karst groundwater flow system and has effects on TDS and Sr2+ content. TDS rises gradually with runoff distance as a whole. In addition, the groundwater nearby Dayugou fault(F21) and southern discharge area have a lower TDS value than that in the surrounding area. This could be the result of groundwater flow at the different geological structure, causing various residence time and interactions between groundwater and aquifer minerals. The intrusive rocks are rich in Sr elements. The groundwater samples investigated neighboring lamprophyre (χ) and magmatic rock (γ), have higher Sr2+ concentrations compared with those from other flow fields. Additionally, anthropogenic activities such as rising exploitation and the usage of ammonium chloride fertilizer also have striking effects on hydrochemical components. This research could provide significant insights into the local governments that can make effective management and protection of karst groundwater in Beijing.