Arsenic contamination in groundwater is pervasive throughout deltaic regions of Southeast Asia and threatens the health of millions. The speciation of As in sediments overlying contaminated aquifers is poorly constrained. Here, we investigate the chemical and mineralogical compositions of sediment cores collected from the Mekong Delta in Vietnam, elucidate the speciation of iron and arsenic, and relate them to the sediment depositional environment. Gradual dissolution of ferric (oxyhydr)oxides with depth is observed down to 7 m, corresponding to the establishment of reducing conditions. Within the reduced sediment, layers originating from marine, coastal or alluvial depositional environments are identified and their age is consistent with a late Holocene transgression in the Mekong Delta. In the organic matter- and sulfur-rich layers, arsenic is present in association with organic matter through thiol-bonding and in the form of arsenian pyrite. The highest arsenic concentration (34–69 ppm) is found in the peat layer at 16 m and suggests the accumulation of arsenic due to the formation of thiol-bound trivalent arsenic (40–55%) and arsenian pyrite (15–30%) in a paleo-mangrove depositional environment (∼8079 yr BP). Where sulfur is limited, siderite is identified, and oxygen- and thiol-bound trivalent arsenic are the predominant forms. It is also worth noting that pentavalent arsenic coordinated to oxygen is ubiquitous in the sediment profile, even in reduced sediment layers. But the identity of the oxygen-bound arsenic species remains unknown. This work shows direct evidence of thiol-bound trivalent arsenic in the Mekong Delta sediments and provides insight to refine the current model of the origin, deposition, and release of arsenic in the alluvial aquifers of the Mekong Delta.