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.