1. Many river dolphin populations are most vulnerable during the low-water season when habitat is limited. Indus River dolphin habitat selection in the dry season was investigated using Generalized Linear Models of dolphin distribution and abundance in relation to physical features of river geomorphology and channel geometry in cross-section. 2. Dolphins selected locations in the river with significantly greater mean depth, maximum depth, cross-sectional area, and hydraulic radius, and significantly narrower river width and a lower degree of braiding than areas where dolphins were absent. They were also recorded with higher frequency at river constrictions and at confluences. 3. Channel cross-sectional area was the most important factor affecting dolphin presence and abundance, with the area of water below 1 m in depth exerting the greatest influence. Indus dolphins avoided channels with small cross-sectional area (<700 m2), presumably owing to the risk of entrapment and reduced foraging opportunities. 4. Channel geometry had a greater ability to explain dolphin distribution than river geomorphology; however, both analyses indicated similar types of habitat selection. The dolphin–habitat relationships identified in the river geomorphology analysis were scale-dependent, indicating that dolphin distribution is driven by the occurrence of discrete small-scale features, such as confluences and constrictions, as well as by broader-scale habitat complexes. 5. There are numerous plans to impound or extract more water from the Indus River system. If low-water season flows are allowed to decrease further, the amount of deeper habitat will decline, there may be insufficient patches of suitable habitat to support the dolphin population through the low-water season, and dolphins may become isolated within deeper river sections, unable or unwilling to traverse through shallows between favourable patches of habitat.