Naturally occurring (i.e., geogenic) ammonium in groundwater has been widely detected globally, but the major controls on its regional distribution have been poorly characterized. Here, we identified the dominant role of paleo-geomorphology driven by paleo-climate in controlling the spatial variability of geogenic ammonium in groundwater using random forest algorithm and revealed the underlying mechanisms based on borehole sediment analysis of data obtained from the Dongting Lake Plain of the central Yangtze River basins in China. In the paleochannel (PC) area, the aquifer depth-matched sediments were deposited during the last deglaciation when warm climate resulted in rapid filling into incised valleys, and terrestrial organic matter (OM) mainly as lignin experienced less degradation prior to sedimentation and had lower humification, higher N abundance, and nominal oxidation state of carbon (NOSC). In the paleo-interfluve (PI) area, the depth-matched sediments were deposited during the last glaciation, followed by intensive erosion in the surface during the last glacial maximum, and terrestrial OM mainly as lignin had been partly degraded into aliphatics prior to sedimentation and had higher humification, lower N abundance, and NOSC. As a result, under the present anaerobic conditions, less-humic and N-rich OM with more oxidized C tends to be more intensively mineralized into ammonium in the PC area than those in the PI area. These findings highlight the importance of paleo-geomorphology with paleo-climate in controlling the enrichment of geogenic ammonium in groundwater, which has a universal significance for understanding the genesis and distribution of high N loads in the aquatic environment worldwide.