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In temperate karst aquifers under intensive anthropogenic impacts and high heterogeneity, groundwater contamination tracking has predominantly focused on nitrate, but inadequate evidence for co-occurring ammonium sources undermines accurate nitrogen pollution assessments. To address this gap, this study pioneers the application of an δ¹⁵N_NH4 isotope approach within the groundwater flow system framework of Jinan Spring Catchment, and constructs a novel ammonium-nitrate isotope tracing system (δ¹⁵N_NH4, δ¹⁵N_NO3 and δ¹⁸O_NO3) for full-form source tracking. This integrated system enables synergistic identification of pollution source for both NH₄⁺-N and NO₃⁻-N, significantly enhancing the resolution of key nitrogen cycling pathways, particularly ammonium-dominated microbial nitrification operating within karst aquifers. Furthermore, we implemented a Bayesian mixing model (Simmr) to quantitatively apportion nitrate sources in karst groundwater. The dominant form of inorganic nitrogen in karst groundwater was NO₃⁻-N (0.4−42.2 mg/L), with 56% of samples exceeding WHO standards (50 mg/L as NO₃⁻), and NO₃⁻-N concentrations demonstrated an overall upward trend from 1958 to 2019. δ¹⁵N_NH4 and nitrate isotope data both confirmed that NH₄⁺-N and NO₃⁻-N primarily originated from ammonium fertilizer and soil nitrogen. The Simmr model also corroborated that ammonium fertilizer (28.4−58.3%) and soil nitrogen (23.1−62.7%) were also primary contributors to groundwater NO₃⁻-N. Hydrochemical and dual nitrogen isotope evidences revealed for the first time that mineralization and re-nitrification of soil nitrogen, nitrification of ammonium fertilizers, and mineralization-immobilization-turnover of nitrate fertilizers all promoted nitrate accumulation in karst groundwater. Groundwater flow analysis revealed that mixing between shallow and deep karst groundwater might constitute the primary mechanism for nitrate attenuation of spring waters in the urban discharge area, with denitrification playing a negligible role. Effective land management measures such as soil erosion control and optimized ammonium fertilizer application should be adopted in the recharge areas. These findings provide new insights into nitrogen behavior in temperate karst groundwater, offering valuable guidance for water resource management and environmental protection in similar karst systems.