In the extensive agro-pastoral ecotone of northern China, groundwater is a valuable resource, but it suffers from severe nitrate pollution. However, the extent of the contributions of agricultural and pastoral activities to nitrate accumulation in the groundwater of the region remains unclear. This study aimed to identify the main sources of groundwater nitrate in Chahannur Basin, a typical agro-pastoral ecotone in the semi-arid zone of northern China, using the MixSIAR model based on dual stable isotopes and dissolved organic matter (DOM) fluorescence. The hydrochemical and isotopic results showed that the groundwater has high concentrations of nitrate (up to 208.19 mg/L) with weak denitrification, and nitrate accumulation is mainly driven by mixed input from different sources. The MixSIAR model results indicated that the largest contributors to groundwater nitrate accumulation are manure & sewage, followed by soil nitrogen, chemical fertilizers, and atmospheric deposition. According to the DOM fluorescence characteristics, the groundwater is strongly affected by livestock and poultry waste, followed by soil humic substances. Moreover, the DOM fluorescence results further supported the MixSIAR model results based on the significant correlation between the contributions of nitrate sources and the percentages of fluorescent components, jointly confirming that the main source of nitrate in groundwater is manure and sewage, followed by soil nitrogen. These findings indicate that coupled evidences from the MixSIAR model and DOM fluorescence could be applied to identify the sources of nitrate in groundwater, and this coupling can provide valuable information for local authorities to achieve sustainable groundwater management.