In order to thoroughly reveal the karst groundwater system in response to the external environment, multi-index high-resolution auto-monitoring instruments were used to research the hydrogeochemistry variations of Qingmuguan subterranean stream. The monitoring indicators were pH value, electrical conductivity (EC), water level, rainfall and NO3-. In the observed 6 times rainfall events, the pH value was mainly controlled by acid rain and EC was impacted by the rain chemistry, physical dilution effect of rainfall and agricultural wastewater. NO3- derived from agricultural activities was less impacted by rain chemistry; and its variations were mainly affected by physical dilution effect of rainfall and agricultural wastewater. Under the influences of the R1 rainfall, the rapid changes of EC and NO3- were contrary in generally, but pH value decreased due to the acid rain. In the R2, R3, R4 and R6 rain events, the water level was positively response to the rainfall and the pH value decreased due to the acid rain; however both of the EC and NO3- decreased due to the dilution effect. With the afflux of agricultural wastewater, both of the EC and NO3- were rapidly changed in synchronization within the shortest of 5 h of and the longest of only 27 h and the pH value showed accelerated decline. During the R5 torrential rain events, water level abruptly increased and all of the pH value, EC and NO3- sharply decreased as a result of dilution effect. The groundwater quality was changed because the afflux of agricultural wastewaters in the entire rainfall periods. According to the National Groundwater Quality Standard, P. R. China (GB/T 14848-9), the groundwater quality of the QSS showed the following order in the entire rainfall events: Grade III --> Grade IV --> Grade V --> Grade 1V --> Grade V --> Grade LV --> Grade V --> Grade IV --> Grade III. As a important drinking water source around local inhabitants, the groundwater quality of Qingmuguan subterranean stream was deteriorated to Grade V in rain-fertilize periods. However, the sampling methods in field did show a simple variation curve. Consequently,the results from the research illustrate the need to redesign hydrochemical sampling methods for karat hydrology system, especially under the impact of human activities.