Divergent Compositions and Biogeochemical Pathways of Dissolved Organic Matter in a Monsoon-Affected Coastal Aquifer: Insights from Molecular Characterization

Coastal groundwater in monsoon-dominated regions faces compounding threats from seasonal hydrological extremes and seawater intrusion (SWI), yet the molecular-scale response of dissolved organic matter (DOM) remains poorly understood. We conducted a two-season investigation in Mannar District, Sri Lanka, integrating hydrochemistry, fluorescence spectroscopy, and Fourier-transform ion cyclotron resonance mass spectrometry to characterize DOM dynamics across shallow and deep groundwater. Dry-season chloride averaged 302 mg/L (shallow—5 to 12 m) and 505 mg/L (tube wells—20 to 30 m), then declined by 60–80% during monsoon recharge. Despite this freshening, DOM dynamics were decoupled from salinity: shallow wells showed dry-season DOC peaks (6.64 mg/L) driven by soil concentration, while tube wells exhibited wet-season enrichment (5.02 mg/L). Shallow aquifers maintained consistently high humification indices (around 0.70) and aromatic-rich DOM, indicating sustained buffering by soil-derived inputs. In contrast, wet-season recharge in tube wells appeared to stimulate microbial processing, as indicated by elevated protein-like fluorescence (C2: 26% to 36%) and a higher contribution of nitrogen-bearing formulas (CHONs: 31.4% to 37.1%). Tube wells also accumulated reduced, energy-rich DOM with correspondingly high molecular lability indices. Paradoxically, correlation networks suggested that these saturated aliphatic and halogenated structures persist due to kinetic protection under low oxygen, high-salinity conditions. These findings indicate that aquifer structure and redox conditions control DOM biogeochemistry in coastal groundwater systems. At the molecular level, DOM dynamics are influenced by aquifer depth and seasonal recharge, leading to a decoupling between salinity and organic matter transformation.