Agricultural and Hydrogeochemical Controls on Nitrate and Sulfate in a Karst Surface Water–Groundwater System

Agricultural karst watersheds are highly vulnerable to nutrient loss because strong surface water–groundwater (SW–GW) connectivity can rapidly transfer nitrogen and sulfur species from soils, agricultural activities, and human settlements into aquatic systems. However, the coupled behavior and contrasting controls of nitrate (NO3−) and sulfate (SO42−) in such agroecosystems remain insufficiently understood, limiting effective nutrient and groundwater-quality management. In this study, a typical karst agricultural watershed in Southwest China was selected to investigate the sources, transformation processes, and transport pathways of NO3− and SO42− under strong SW–GW interactions. During the rainy season, 44 groundwater and 40 surface water samples were collected for major hydrochemical and nitrate–sulfate stable isotope analyses. An integrated framework combining hydrochemical analysis, self-organizing maps (SOM), positive matrix factorization (PMF), and MixSIAR were used to identify dominant sources, quantify source contributions, and clarify controlling processes. The results showed that groundwater was mainly characterized by carbonate-controlled Ca-HCO3 facies, whereas surface water exhibited higher mineralization and a shift toward Ca-SO4 facies, indicating stronger external inputs and rapid hydrological responses. Nitrate was primarily controlled by external nitrogen inputs, with manure and sewage and soil nitrogen contributing 39–62% and 16–33%, respectively. Nitrate was also regulated by nitrification under oxic conditions, while denitrification was negligible. In contrast, sulfate was predominantly governed by geogenic processes, with sulfide oxidation contributing 63–83%, while other sources were minor. These contrasting controls resulted in distinct spatial and process behaviors: nitrate showed source-driven variability associated with agricultural and domestic inputs, whereas sulfate displayed process-driven accumulation mainly controlled by water–rock interactions. Strong SW–GW connectivity enhanced the transfer of anthropogenic nutrient signals, while subsurface mixing and buffering regulated their expression in groundwater and surface water. These findings demonstrate a clear decoupling between nitrate and sulfate controls in agricultural karst systems and provide a scientific basis for nutrient pollution control, groundwater protection, and sustainable agricultural water management in vulnerable karst regions.