The June 2013 disaster in Kedarnath hit the Mandakini–Alaknanda river valley, resulting in devastating floods. This study deals with the pre- and post-flood event changes in the channel morphology and aims to investigate the geomorphological processes under river management in the Alaknanda valley, NW Himalaya and how the hydroelectric reservoir may have impeded the natural impact of the disaster and created geomorphic discontinuity. This work analyses the spatio-temporal variations in channel morphology over the last decade 2010–2020, discussing the impact of 2013 extreme event; the role of gradient in morphological patterns in river basin system. It highlights how the channel parameters like the thalweg shifts, active channel width, and area under sedimentation responded, from headwaters to lower gradient Lesser Himalayan zones to the 2013 event and suggests that any positive changes in these parameters diminish soon after the reservoir. The study implies that the capability of the reservoir to adjust the sediment load of the event in its upstream is an immediate short-term effect, but brings out the fact that it creates a geomorphic disconnect in the channel between upstream and downstream channel reaches of the reservoir. This disconnect may have a negative impact on sediment storage and sediment–water routing of the river and should be factored into the dam design ensuring natural continuum of geomorphic processes. Further, the study argues that the terrain north of the Main Central Thrust (Higher Himalaya) should be kept free from major human interventions to reduce flood hazards.