A 1.3-km-thick section of basin-fill sediments within the Skardu intermontane basin of the Karakoram Himalaya, termed the Bunthang sequence, is predominantly reversely magnetized. Glacial deposits and landforms are closely associated with the Bunthang sequence. This implies that basin filling took place between glacial advances and prior to the present Brunhes normal chron, i.e., between 3.2 and 0.73 Ma. Four major facies interfinger within the Bunthang sequence: glacial facies; lacustrine facies, indicative of periods during which the Indus River was ponded within the basin; aggradational fluvial facies that represent periods during which the gradient of the Indus River was controlled by rising base level downstream; and alluvial fanglomerates that prograde transversely from the basin margin into the basin at different stratigraphic levels. The last facies represents periods of decreased sedimentation by the Indus River relative to alluvial sedimentation from the basin margin. Downstream from the Skardu Basin, the Indus River crosses the Nanga Parbat–Haramosh syntaxis; this is an area of rapid late Cenozoic uplift (as much as 1 cm/yr). Differential uplift of the Nanga Parbat–Haramosh syntaxis relative to its surrounding terrain led to local variations in Indus River gradient. Temporary ponding of the Indus River is inferred to have occurred when the uplift rate of the Nanga Parbat–Haramosh syntaxis exceeded the rate of downcutting by the Indus River. Temporary blockage of the Indus River Gorge through the Nanga Parbat–Haramosh syntaxis by glaciers or by major landslides may also have led to variations in base level. Temporal variations in the gradient and base level of the Indus River downstream from the Skardu Basin, are reflected in the different facies that interfinger within the Bunthang sequence at Skardu.