A catastrophic storm occurred in Fangshan District of Beijing on 21 July, 2012, which is 60-year storm with the total rainfall of 228mm. After this storm, the various water elements of karst water system in the Heilongguan Spring Basin an active response. This paper analyzed the recharge, runoff and discharge of the groundwater system of the Heilongguan Spring Basin based on karst groundwater level, local geological structure and geomorphical codition, and studied the response to the flood occurred on 21 July, 2012 by analyzing the change of the groundwater level, river flow, spring flow karst groundwater quality after the flood. After the rainfall, the flow reached 221 m3 /s on the Dashihe River, the number of samples with sulfate ion significantly increased. In the Heilongguan Spring Basin, the observed spring flow were 0.305m3 /s on 15 July and 0.30 m3 /s in the morning on 21 July, which reached 3.4734 m3 /s on 25 July and decreased to 2.34 m3 /s 29 July. The flow changed greatly, which is related to the supply from the Dashihe River to the karst water.