Groundwater arsenic (As) presents a public health risk of great magnitude in densely populated Asian delta regions, most acutely in the Bengal Basin (West Bengal, India and Bangladesh). Research has focussed on the sources, mobilization, and heterogeneity of groundwater As, but a consistent explanation of As distribution from local to basin scale remains elusive. We show for the Bengal Aquifer System that the numerous, discontinuous silt-clay layers together with surface topography impose a hierarchical pattern of groundwater flow which constrains As penetration into the aquifer and controls its redistribution towards discharge zones, where it is re-sequestered to solid phases. This is particularly so for the discrete periods of As release to groundwater in the shallow sub-surface associated with sea level high-stand conditions of Quaternary inter-glacial periods. We propose a hypothesis concerning groundwater flow (SIHA: Silt-clay layers Impose Hierarchical groundwater flow patterns constraining Arsenic progression) which links consensus views on the As source and history of sedimentation in the basin to the variety of spatial and depth distributions of groundwater As reported in the literature. SIHA reconciles apparent inconsistencies between independent, in some cases contrasting, field observations. We infer that lithological and topographic controls on groundwater flow, inherent to SIHA, apply more generally to deltaic aquifers elsewhere. The analysis suggests that groundwater arsenic may persist in the aquifers of Asian deltas over thousands of years, but in certain regions, particularly at deeper levels, arsenic will not exceed low background concentrations unless groundwater flow systems are short-circuited by excessive pumping.