Karst regions are composed of soluble rock, often limestone, which leads to the formation of fissures, sinkholes and water flow conduits such as caves. Pollutants in karst waters tend to be quickly directed and concentrated into these subsurface conduits. As a result of this and other factors, water resources are especially sensitive to contamination and pollution in karst areas. Pollutant concentrations going into fluvial systems travelling through the subsurface in karst areas are often very similar to the concentrations arriving at outlets such as springs. Areas connected by karst conduit flows must be distinctly determined and special attention should be given to water quality impacts from land-use practices near conduit inputs. The climate which affects a certain karst area can also have different impacts on water resources considerations. For example, in the temperate climate of Kentucky precipitation is essentially even in distribution throughout the year. In contrast, southwest China is affected by a monsoon climate with high precipitation in the spring to summer and drier conditions in other seasons. In the wet season large storm pulses can effectively transport contaminants to water sources resulting in loads that can be unhealthy for frequent human consumption in drinking water. The dry seasons can be particularly severe in karst areas as water quickly drains to the subsurface, making water access a major hardship. The research for this study focused on the seasonal influences that the climate of southwest China poses for water quality, including differences in pesticide concentrations between agricultural and residential areas hydrologically linked by karst conduits. In late 2007 the fluvial connections in a simple karst system near Chongqing were confirmed using dye tracing techniques. Once these connections were established and the flow of the subterranean stream was assessed, the transport of agricultural runoff in the system was studied. Data loggers were used to record continuous data of the water conditions, including nitrate concentrations. The pesticides in the agricultural runoff entering and exiting the subterranean stream were quantified using ELISA methods. The concentrations were found to be within safe limits for drinking water. The hypothesis that there is a close relationship between concentrations of the pesticides glyphosate, chlorothalonil, and triazines in the input and the output of the system was supported by the results. When considering the hydrology and water chemistry data of the site, along with the water samples tested for pesticides, non-parametric statistical testing showed the correlations between these factors to be significant with p\u3c0.01. The percent difference between the input and the output concentrations of glyphosate, chlorothalonil, and triazines were 31, 43, and 57% respectively. Taking into account the rapid and direct flows in this karst system, the concentrations of the pesticides found in the output were more similar to the input than would be expected in a surface stream. This suggests that there are fewer natural remediation effects reducing contamination in subsurface karst rivers of southwest China than in surface rivers. Therefore, these systems should be handled with extra attention to possible contamination of water resources. The research was conducted in the spring and summer of 2007-2008 and funded by the U.S. Agency for International Development