With a fixed supplied scope and resource elements, karst groundwater system circulates as an independent unit in northern China, which controls karst water transport and enrichment, hydrochemical evolution, composition of water resources and environmental geological problems. In order to carry out karst groundwater system research, the primary task is determining the location and hydrogeological properties of boundaries. In this paper, we choose Heilongguan karst water system at Xishan region in Beijing as research object and determine the hydrogeological boundaries by geology, karst dynamics, fluid dynamics, hydro-geochemical, geophysical exploration and other methods. Finally, we conclude that Heilongguan karst water system is composed of two subsystems. The one is Dashihe anticline karst water subsystem, situated in the south and composed by the Upper Proterozoic aquifer;The other is Baihuashan syncline karst water subsystem, situated in the north and composed by Cambrian-Ordovician aquifer. According to hydrogeological properties of boundaries, there are surface water watershed boundary, underground watershed boundary, confining boundaries, karst aquifers deep stagnant boundary and other types.