Drinking shallow groundwater with naturally elevated concentrations of arsenic is causing widespread disease in many parts of South and Southeast Asia. In the Bengal Basin, growing reliance on deep (>150 m) groundwater has lowered exposure. In the most affected districts of Bangladesh, shallow groundwater concentrations average 100 to 370 μg L−1, while deep groundwater is typically < 10 μg L−1. Groundwater flow simulations have suggested that, even when deep pumping is restricted to domestic use, deep groundwater in some areas of the Bengal Basin is at risk of contamination. However, these simulations have neglected the impedance of As migration by adsorption to aquifer sediments. Here we quantify for the first time As sorption on deeper sediments in situ by replicating the intrusion of shallow groundwater through injection of 1,000 L of deep groundwater modified with 200 μg L−1 of As into a deeper aquifer. Arsenic concentrations in the injected water were reduced by 70% due to adsorption within a single day. Basin-scale modelling indicates that while As adsorption extends the sustainable use of deep groundwater, some areas remain vulnerable; these areas can be prioritized for management and monitoring.