The hydrogeochemical characteristics of groundwater are an important element in the study of the spatial and temporal variation of groundwater resources, which is crucial to water resources utilization, ecological environmental protection, and human development. Water samples were collected at eight observation of Nandong Karst Water System (NKWS) sites in each month of 2019, and the main ions and isotopes of the water samples were examined. The hydrogeochemistry characteristics of groundwater and its differences with surface water were explored by using the methods of multivariate statistics, Gibbs model. Results showed that the water chemistry types of groundwater were mainly HCO3 – Ca and HCO3 –Ca· Mg. The analysis of hydrogen and oxygen isotope showed that the initial recharge source of surface water and groundwater were atmospheric precipitation, and the measured hydrogen and oxygen isotopes of surface water were heavier due to the strong evaporation effect. The natural and anthropogenic processes contributed to the chemical composition of surface water and groundwater in the study area. However, the main factor affecting the quality of surface water and groundwater was the input of anthropogenic contaminants. In terms of natural factors, the main chemical ions of surface water and groundwater were mainly controlled by water–rock action originating from weathering and hydrolysis of rocks and soils. Ca2+, Mg2+, and HCO− 3 mainly originated from natural dissolution of carbonate rocks. K+, Na+, SO2− 4, and Cl− were partly from atmospheric precipitation. For human activities, Na+ and Cl− were partly from domestic water for local residents. SO2− 4 in surface water mainly came from mining. NO− 3 in groundwater mainly came from chemical fertilizers, and NO− 3 in surface water were mainly from human waste and domestic sewage.

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Wastes from social economic activities had great impact on water quality thereby limiting water usability for domestic purposes. Sewages discharge from people activities, usually consist of undesirable concentrations of soluble chemicals that infiltrate into the surrounding surface and underground water, and then constitute health risk to the populace. In order to investigate the concentration characteristics and health risk for the local residents in Nandong Underground River Watershed (NURW), eleven common heavy metals in the water body analysis were conducted. Health risk assessment (HRA) was taken to analyze eleven heavy metals of 84 water samples from surface and underground waters in NURW: 36 samples underground water and 48 samples surface water. Our results showed that the heavy metals concentration order is that of Fe > Al > Mn > Zn > As > Cd > Pb > Cr > Ni > Cu > Hg. Correlation analysis indicates that these eleven metal elements have certain similarity on material source and migration transformation. The health risks for local residents exposed to metal elements in the water of NURW mainly from carcinogenic risk (10−6～10−4 a−1) through drinking way, and the health risk of heavy metals exposed to children through drinking way was much higher than adults. The maximum exposing health risks of Cr in both underground and surface water were higher than the recommendation standard (5.0×10-5 a-1) from ICRP, and all the values over the standard (5.0×10-6 a-1) recommended by the Swedish Environmental Protection Agency and the Dutch Ministry of Construction and Environment and the British Royal Society. The results of health risk assessment shows that Cr in the water of NURW was the mainly source of carcinogenic risk for the local residents, following by Cd and As. Consequently, it is necessary to control the three carcinogenic metals when the water was used as drinking water source.