Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010–2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5–510 μg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 μg/L for the studied period of 2010–2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations.