The characteristics of dissolved organic matter (DOM) serves as indicators of nitrate pollution in groundwater. However, the specific DOM components associated with nitrate in groundwater systems remain unclear. In this study, dual isotopes of nitrate, three-dimensional Excitation emission matrices (EEMs) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was utilized to uncover the sources of nitrate and their associations with DOM characteristics. The predominant nitrate in the targeted aquifer was derived from soil organic nitrogen (mean 46.0%) and manure &sewage (mean 34.3%). The DOM in nitrate-contaminated groundwater (nitrate-nitrogen > 20mg/L) exhibited evident exogenous characteristics, with a bioavailable content 2.58 times greater than that of uncontaminated groundwater. Regarding the molecular characteristics, DOM molecules characterized by CHO + 3N, featuring lower molecular weights and H/C ratios, indicated potential for mineralization, while CHONS formulas indicated the exogenous features, providing the potential for accurate traceability. These findings provide insights at the molecular level into the characterization of DOM in nitrate-contaminated groundwater and offer scientific guidance for decision-making regarding the remediation of groundwater nitrate pollution.