Environmental isotopes and 14C dating were applied to estimate ages and recharge sources of deep groundwater (⩾150 m bgl) in south-east Bangladesh. With one exception, deep groundwater is shown to have been recharged more recently than 10 Ka (range 3–9 Ka, mean 7.6 Ka), under climatic conditions indicated by δ18O and δ2H as similar to the present day. Groundwater age distributions have been used to infer the scale of aquifer hydraulic anisotropy. 2D groundwater flow modelling is able to reproduce the observed vertical profiles of groundwater age, as determined at two locations, when the aquifer is assigned a permeability anisotropy (Kx/Kz) of at least 103. Under these conditions, deep groundwater originates as recharge in the hill regions at the eastern boundary of the basin. Recharge rates estimated from the groundwater ages are close to an estimate of the current rate of deep groundwater abstraction. Cautious development and careful monitoring are therefore necessary, as excessive deep groundwater pumping could draw dissolved arsenic from the shallow levels of the Bengal Aquifer System (BAS) and contaminate the deep groundwater resource.