Surface processes involve complex feedback effects between tectonic and climatic influences in the high mountains of Pamir. The ongoing India–Asia collision provokes the development of east–west-trending mountain ranges that impose structural control on flow directions of the Pamir rivers. The evolving relief is further controlled by strong moisture gradients. The decreasing precipitations from the southern and western margins of the Pamir Plateau to its center, in their turn, control the emplacement of glaciers. Chronologies of glacial records from the Pamir Plateau attest for strong climatic variability during the Quaternary. Corresponding remnants of glacial advances suggest glacial morphodynamic restricted to >4,000 m a.s.l. since marine isotope stage 4. The Panj, the trunk river of Pamir, deflects from the predominant westward drainage, connecting its main tributaries at the western margin of the drainage basin. The geometry of the river network and the pattern of incision characterize the Panj as a composite river. River reaches of indicated low incision coincide with west-trending valleys, parallel to domes and their bounding faults. Valley shape ratios reflect increased incision in north-trending sections, but do not match with changes in the catchment geometry or erodibility of rock types. Modelled riverbed profiles distinguish three Panj reaches. The upstream increase in convexity suggests successive river captures in response to local base-level changes. The northward-deflected river reaches link the local base levels, which coincide with the southern boundaries of the Shakhdara and Yazgulom Dome and Darvaz Range. We argue that tectonics plays a large role controlling the drainage system of the Panj and hence surface processes in the Pamir mountains.