The aim of this study was to explore the chemical characteristics of surface water and groundwater, and the contribution of various salts to the main ions. Karst small watershed was taken as the research scale, field monitoring and sampling, and laboratory experiments for surface water and groundwater chemistry in Shuanghe Cave area was carried out. SPSS statistical software was used to analyze the principal components of water samples. The results were as follows: (1) Ca2+ and Mg2+ were the predominant cations of groundwater and surface water in Shuanghe Cave, and the predominant anions were HCO3- and SO42-. The water chemistry could be classified as Ca2+?Mg2+—HCO3- type, but Gypsum Cave was Ca2+?Mg2+—SO42- type. The contents of most ions varied with different sampling points, seasons and types of water; (2) Gibbs and triangular diagrams analyses revealed that the water compositions in the watershed were significantly impacted by rock weathering process. The main anions were derived from carbonate dissolution and evaporation, weathered rock or rock salt. Evaporation salt dissolution was the main controlling mechanism of cation, and the effect of silicate weathering and erosion also affected regional ion change; (3) The principal component analysis showed that the degree of influence on the regional composition of ion chemistry followed the order of carbonates＞evaporites＞silicates. Among them, the influence of H2CO3 weathering carbonate rock was obvious, but in certain underground river, water chemistry was mainly affected by H2SO4 weathering carbonate rock. In addition, agricultural and domestic activities also showed some impacts on water characteristics. The results of this study have a great significance for the protection, development, and utilization of water resources in Shuanghe Cave and for karst carbon cycle research.