The Nandong Underground River System (NURS) is located in a typical karst agriculture dominated area in the southeast Yunnan Province, China. Groundwater plays an important role for social and economical development in the area. However, with the rapid increase in population and expansion of farm land, groundwater quality has degraded. 42 groundwater samples collected from springs in the NURS showed great variation of chemical compositions across the study basin. With increased anthropogenic contamination in the area, the groundwater chemistry has changed from the typical Ca-HCO(3) or Ca (Mg)-HCO(3) type in karst groundwater to the Ca-Cl (+NO(3)) or Ca (Mg)-Cl (+NO(3)), and Ca-Cl (+NO(3)+SO(4)) or Ca (Mg)-Cl (+NO(3)+SO(4)) type, indicating increases in NO(3)(-), Cl(-) and SO(4)(2-) concentrations that were caused most likely by human activities in the region. This study implemented the R-mode factor analysis to investigate the chemical characteristics of groundwater and to distinguish the natural and anthropogenic processes affecting groundwater quality in the system. The R-mode factor analysis together with geology and land uses revealed that: (a) contamination from human activities such as sewage effluents and agricultural fertilizers; (b) water-rock interaction in the limestone-dominated system; and (c) water-rock interaction in the dolomite-dominated system were the three major factors contributing to groundwater quality. Natural dissolution of carbonate rock (water-rock interaction) was the primary source of Ca(2+) and HCO(3)(-) in groundwater, water-rock interaction in dolomite-dominated system resulted in higher Mg(2+) in the groundwater, and human activities were likely others sources. Sewage effluents and fertilizers could be the main contributor of Cl(-), NO(3)(-), SO(4)(2-), Na(+) and K(+) to the groundwater system in the area. This study suggested that both natural and anthropogenic processes contributed to chemical composition of groundwater in the NURS, human activities played the most important role, however.