The elevated levels of geogenic (natural) ammonium in groundwater have been frequently documented in recent years. Although improving insights have been achieved in understanding the genesis of ammonium in the subsurface environment, the vertical variability of the geogenic ammonium in groundwater remains poorly understood. Here, we selected typical multi-layered aquifer systems in the central Yangtze River plain and characterized the vertical heterogeneity of geogenic ammonium through the hydrogeochemical analysis. Subsequently, the controlling factors were identified by examining the molecular composition of dissolved organic matter (DOM) and aquifer sediment features. The results indicated that the ammonium concentration in groundwater increased from the deep to shallow aquifers (2.13 to 9.88 mg/L as N), accompanied by a transition in organic matter (OM) degradation towards the methanogenic stage (δ13C-DIC: -23.07 to -0.34‰). Compared to the deeper aquifers, the DOM in the shallow aquifer was characterized by a higher abundance of the N-containing OM (15.1% > 13.13% > 12.76%) with a lower molecular lability index, corresponding to more thorough degradation extent. The characteristics of the soluble OM in depth-matched sediments were similar to those of the DOM in groundwater, suggesting the persistent water-rock interactions. Besides, the pumping tests revealed that the hydraulic conductivity decreased from deep to shallow aquifers (2.28 to 0.62 m/d), which further facilitated the more retention of geogenic ammonium in the shallow aquifer. That is, the combined effects of the abundant N-containing OM in sediments, strong degradation of the bioactive DOM, and long retention governed by hydrodynamics contributed to the increased ammonium enrichment in the shallow aquifer, thereby generating the vertical variability. The findings underscore the significance of the complex coupled factors in controlling the vertical distribution of geogenic ammonium in multi-layered aquifer systems, which was crucial for understanding the spatial heterogeneity of geogenic contaminated groundwater.
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