Although groundwater nitrogen pollution has been widely studied, the control of hydrogeological conditions on behavior of nitrogen compounds has been poorly understood. In this study, multiple stable isotopes (N/C/H/O), spectral characteristics of DOM coupled with water chemistry were used to reveal the sources and fate of nitrate and ammonium in three subareas with different hydrogeological conditions in the Central Yangtze River Basin. We identified three contrasting patterns of nitrogen sources and fate in groundwater controlled by different aquifer features. In a reducing porous aquifer mainly composed of carbonate minerals overlain by a thick low-permeability layer, the NH₄–N concentration is high (mean 4.12 mg/L) but with quite low NO₃–N concentration (mean 0.28 mg/L). The high ammonium is mainly from intense degradation of organic matter (OM), while denitrification at a higher rate results in nitrate removal. Feammox may be favored owing to abundant humics acting as the electron shuttle. In a weakly reducing to oxidizing porous aquifer mainly composed of aluminosilicate minerals overlain by a varying thickness of low-permeability layer, high ammonium occurs in a weakly reducing condition and is affected by both anthropogenic input and OM degradation, while high nitrate occurs in a more oxidizing condition and could be mainly from soil nitrogen, manure or sewage. Feammox may be also favored due to more acidic environment formed by weathering of aluminosilicate minerals, fluctuating redox condition and low abundance of labile organic carbon, while denitrification occurs at a slower rate coupled with concurrent re-oxidation of nitrite to nitrate. In an oxidizing porous - fissured aquifer system overlain by a thin low-permeability layer, the concentrations of ammonium and nitrate are both low, possibly due to strong hydrodynamic and flushing condition, although slightly higher concentration of nitrate exhibit similar sources and fate with the weakly reducing to oxidizing porous aquifer mentioned above.