Groundwater recharge source and flowpaths, along with aquifer medium characteristics, are identified based on nitrate distribution and dynamics. These are significant factors in long-term water-resources management of the Sichuan-Yunnan-Guizhou lead-zinc mining deposits, southwestern China. The results show that high nitrate concentration correlates with lower temperature and heavy isotope enrichment, indicating groundwater recharge from the eastern karst depression area (situated at higher elevation), which has intensive agriculture. Higher NO3- concentration corresponds to higher Ca/Mg ratio in the Carboniferous karst aquifer, both indicating the preferential groundwater flowpath, while the lateral nitrate distribution signifies hydraulic connection with the northern Devonian aquifer passing through the aquitard via NE–SW and N–S trending faults. Nitrate pollution has reached deep sections of the karst aquifers and generated a wide vertical distribution, with the lowest elevation of significant nitrate concentration at –28 m relative to sea level, far lower than the recharge area by over 1,500 m. The variations in groundwater temperature, electrical conductivity and partial pressure of CO2 in the early rainy season are associated with enhanced dissolution capacity of the carbonate minerals, controlled by the soil CO2 effect, hence characterizing the mining area as a fissure-dominant karst groundwater system. Under such conditions, nitrate concentration rises and recedes subsequent to recharge events, and these processes characterize nitrate leaching. Overall, the current nitrate distribution is the result of increased agricultural productivity, intensive mine dewatering works and intrinsic media heterogeneity. Nitrate functions as an artificial, stable and cost-effective tracer for groundwater-system characterization in this mining area