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In alluvial aquifers with near-neutral pH and high dissolved arsenic (As) concentrations, the presence and character of sedimentary organic matter (SOM) regulates As mobility by serving as an energetically variable source of electrons for redox reactions or forming As–Fe-OM complexes. Near tidally and seasonally fluctuating rivers, the hyporheic zone (HZ), which embodies the mixing zone between oxic river water and anoxic shallow groundwater, may precipitate (or dissolve) iron (Fe)-oxides which sequester (or mobilize) As. To understand what is driving the mobilization of As within a shallow aquifer and riverbank sands adjacent to the tidally fluctuating Meghna River, we characterized the chemical reactivity of SOM from the sands, and a silt and clay layer, underlying the HZ and aquifer, respectively. Dissolved As (50–500 μg/L) and Fe (1–40 mg/L) concentrations increase with depth within the shallow aquifer. Similar vertical As and Fe concentration gradients were observed within the riverbank sands where concentrations of the products of reductive dissolution of Fe-oxides increase with proximity to the silt layer. Compared to all other sediments, the SOM in the clay aquitard contains older, more recalcitrant, terrestrially-derived material with high proportions of aromatic carboxylate functional groups. The shallow silt layer contains fresher SOM with higher proportions of amides and more labile polysaccharide moieties. The SOM in both the riverbank and aquifer is terrestrially-derived and humic-like. The labile SOM from the silt layer drives the microbially mediated reductive dissolution of As-bearing Fe-oxides in the HZ. In contrast, the carboxylate-rich SOM from the clay aquitard maintains dissolved As concentrations at the base of the aquifer by complexing with soluble As and Fe. This highlights that SOM-rich fine (silt or clay) layers in the Bengal basin drive As and Fe mobility, however, the specific processes mobilizing As and Fe depend on the lability of the SOM.