Confining clay layers typically protect groundwater aquifers against downward intrusion of contaminants. In the context of groundwater arsenic in Bangladesh, we challenge this notion here by showing that organic carbon drawn from a clay layer into a low-arsenic pre-Holocene (>12 kyr-old) aquifer promotes the reductive dissolution of iron oxides and the release of arsenic. The finding explains a steady rise in arsenic concentrations in a pre-Holocene aquifer below such a clay layer and the repeated failure of a structurally sound community well. Tritium measurements indicate that groundwater from the affected depth interval (40–50 m) was recharged >60 years ago. Deeper (55–65 m) groundwater in the same pre-Holocene aquifer was recharged only 10–50 years ago but is still low in arsenic. Proximity to a confining clay layer that expels organic carbon as an indirect response to groundwater pumping, rather than directly accelerated recharge, caused arsenic contamination of this pre-Holocene aquifer.

Across South Asia, millions of villagers have reduced their exposure to high‐arsenic (As) groundwater by switching to low‐As wells. Isotopic tracers and flow modeling are used in this study to understand the groundwater flow system of a semi‐confined aquifer of Pleistocene (>10 kyr) age in Bangladesh that is generally low in As but has been perturbed by massive pumping at a distance of about 25 km for the municipal water supply of Dhaka. A 10‐ to 15‐m‐thick clay aquitard caps much of the intermediate aquifer (>40‐ to 90‐m depth) in the 3‐km²study area, with some interruptions by younger channel sand deposits indicative of river scouring. Hydraulic heads in the intermediate aquifer below the clay‐capped areas are 1–2 m lower than in the high‐As shallow aquifer above the clay layer. In contrast, similar heads in the shallow and intermediate aquifer are observed where the clay layer is missing. The head distribution suggests a pattern of downward flow through interruptions in the aquitard and lateral advection from the sandy areas to the confined portion of the aquifer. The interpreted flow system is consistent with³H‐³He ages, stable isotope data, and groundwater flow modeling. Lateral flow could explain an association of elevated As with high methane concentrations within layers of gray sand below certain clay‐capped portions of the Pleistocene aquifer. An influx of dissolved organic carbon from the clay layer itself leading to a reduction of initially orange sands has also likely contributed to the rise of As.