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The arsenic-contaminated groundwater has attracted attention in much south and southeast Asian deltas, however, mainly on the deep aquifers. Here, arsenic (As) concentration and its fractionation of the sediment cores in a shallow aquifer in Bangladesh were investigated using ICP-MS, FE-EPMA, XRD and 14C-AMS chronology techniques. The results of the present study indicated that the peak concentrations of As (54.7–79.1 µg/g) were in peat layers (at a depth of 7.5–8.0 m). Several types of iron (oxyhidr)oxides and framboidal pyrite, which contain As also, were found in the peat samples. The high concentrations of As were in an exchangeable form, As-bearing iron crystalline and As-bearing organic materials. We revealed that the As-rich peat layers were formed from 3170 to 3901 cal yrs before, due to the sea level decrease in this area. The 16S rRNA gene-based phylogenetic analysis revealed that the bacterial strains in the As-rich peats were mainly affiliated with genera Acinetobacter, Enterobacter, Escherichia, Bacillus, Clostridiaceae and Acinetobacter. The geo-accumulation index (Igeo) and ecological risk index assessment were calculated for the sediments, which shows that As-rich sediment layers were in range of moderately to heavily contaminated and considerable classes, respectively. Under the permanent saturated condition, the As-rich peat layers should be considered as an important potential driver of the groundwater As in this area. [ABSTRACT FROM AUTHOR]