The Himalaya, the Earth's largest active orogen, produces a deep but relatively unexplored foreland basin by loading the Indian Plate. Newly available two-dimensional seismic data (ca. 5,180 line km) spanning 900 km of the Nepali lowlands allow mapping and interpretation of several regional subsurface markers in two-way-travel time and estimated depth. Isopach maps for the major intervals allow us to interpret the interplay between basement structure, flexure, and faulting within the Ganga Basin. The Indian continental lithosphere beneath the foreland basin contains basement ridges oriented at high angles to the thrust belt. These basement structural highs and intervening depressions, tens to hundreds of kilometres wide, influenced deposition of the Precambrian Vindhyan strata and overlying Paleozoic to Mesozoic successions. The overlying Miocene to Quaternary foreland basin shows along-strike thickness variations across the basement features. Because the foreland basin sediments were mainly deposited in an alluvial plain close to sea-level, accommodation, and therefore thickness, was predominantly controlled by subsidence of the Indian Plate, providing evidence that the basement features controlled foreland basin development. Subsidence varied in time and space during Neogene basin development. When combined with flexural modelling, these observations imply that the subsidence history of the basin was controlled by inherited lateral variations in the flexural rigidity of the Indian Plate, as it was translated northward beneath the Himalayan Orogen. Basement features continue to play a role in higher levels of the thrust belt, showing that basement features in a down-going plate may produce non-cylindrical structures throughout orogen development.