Geogenic ammonium in groundwater owing to mineralization of natural organic matter (NOM) has been reported in different geologic settings, but detailed mechanisms responsible for high ammonium concentration levels are poorly understood. To this end, we chose Quaternary high ammonium aquifer systems in central Yangtze River basins and used carbon isotopes in both dissolved organic carbon and inorganic carbon, together with characterization of dissolved organic matter (DOM) and groundwater chemistry to reveal mechanisms related to the genesis of ammonium. The results indicate that high levels of geogenic ammonium (up to 33.50 mg/L as N) occur due to long-term water-rock interactions in a relatively sluggish hydrogeological environment with abundant organic matter that is rich in both C and N. The stable carbon isotope data suggest that ammonium in the groundwater is released from intensive degradation of organic matter with higher contents of ammonium associated with methanogenesis. The optical signatures of DOM indicate ammonium in the groundwater is mostly associated with terrestrial humic-like components rather than protein-like components. Molecular characterization of DOM by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) shows that, compared to low ammonium groundwater, high ammonium groundwater has larger mass weights, greater abundance of CHO+N compounds, higher percentages of lignin- and condensed-hydrocarbon-like components, lower H/C ratios, higher nominal oxidation state of carbon (NOSC) values, and more double bonds, rings, and aromatic structures. Strong degradation of NOM and preferential utilization of energetically more favorable, terrestrial humic-like components (lignin-like as the main class) with high NOSC values facilitates the formation of high ammonium groundwater. To the best of our knowledge, this is the first effort to use carbon isotopes and DOM characteristics to identify enrichment mechanisms for geogenic ammonium in alluvial-lacustrine aquifer systems.