In the Bengal Basin of Bangladesh and West Bengal (India), where arsenic (As) and salinity adversely affect groundwater in shallow aquifers (<150 m deep), consumers increasingly turn to "the deep aquifer" as a source of low-As and low-salinity water.We show that "the deep aquifer," which has traditionally been regarded as a single entity, can be divided into at least eight deep aquifer units each with distinctive chemical, isotopic, hydraulic, and piezometric characteristics. Except in the rapidly subsiding Sylhet Basin, the deep aquifers are largely As-safe (<50 μg/L and mostly <10 μg/L) but differ in terms of iron (Fe), manganese (Mn), salinity, stable isotopic composition, groundwater age, and in their piezometric response to pumping. We use isotopic data to identify recharge from five periods, of which two are quantitatively dominant: (a) from the Last Glacial Maximum, isotopically heavy water (δ 18 O >−3.5‰) with low As, Cl, and Fe concentrations occupies hydraulically trapped positions in the South-Central, Southeast, Southwest, and Madhupur aquifer units and (b) terminal Pleistocene to Early Holocene recharge of isotopically lighter water (δ 18 O <−3.5‰) that has high Fe and slightly elevated Cl concentrations and was recharged along palaeochannels that facilitated deep circulation up to the mid-Holocene. Piezometric responses to development change in style towards the coast. In the north, water levels at all depths tend to be coincident and transition through a seasonally divergent pattern to become parallel in the south with a near constant downward gradient. The delineation of the deep aquifer units provides a practical framework for the assessment and management of groundwater resources for water supply.