To investigate the characteristics, sources, and transformation patterns of nitrate pollution in subsidence-induced water-logged areas with high water tables, this study focused on typical water-logged areas (open and closed types) in the Huainan mining district. The research employed a comprehensive approach combining water chemistry analysis, stable isotope tracing techniques for hydrogen, oxygen, and nitrate nitrogen, along with Cl- tracing methods and the Bayesian mixing model (MixSIAR). The results indicate that the water chemistry and hydrogen and oxygen isotope characteristics of the two types of subsidence-induced waterlogged areas show significant differentiation. Open-type waterlogged areas are significantly influenced by atmospheric precipitation and groundwater recharge, resulting in rapid water renewal, whereas closed-type waterlogged areas exhibit stronger evaporation and distillation processes, leading to slower water renewal. Nitrate pollution in the study area is jointly regulated by human activities and hydrological processes; in both types of waterlogged areas, soil organic nitrogen, domestic sewage, and livestock manure are the primary sources. In open waterlogged areas, nitrate exhibits characteristics of non-point source diffusion, while in closed waterlogged areas, nitrate accumulation is primarily driven by external input and internal regeneration. Nitrification dominates in both types of waterlogged areas, while denitrification is relatively weak. In open waterlogged areas, fecal wastewater is the primary contributor to nitrate (45%~72%). In enclosed waterlogged areas, nitrogen fertilizers are the primary contributor (23%~52%). The study indicates that differences in water body hydrological exchange conditions, nitrogen migration pathways, and geochemical processes are key factors regulating the structure of nitrate sources. The findings provide a theoretical reference for the management of nitrate pollution in similar coal mining subsidence waterlogged areas.