Mountain streams are frequently characterized by step–pool morphology that provides stability and energy dissipation to the channel network. Large flooding events can overturn the equilibrium of the step–pool condition by altering the entire configuration. This work focuses on the impact of the “Vaia” storm (27–30 October 2018) on a step–pool mountain stream (Rio Cordon, Northeast Italy) and on its evolution after two years of ordinary flow conditions. To achieve the aims, this work uses both remote sensing data (LiDAR and UAV) and direct field measurements (i.e., longitudinal profiles and grain sizes distributions) performed pre-event, post-event, and 2 years later (current conditions). The results show a significant widening (width +81%, area +68%) and the creation of a new avulsion after the storm and a substantial change between the number of units (51 in the pre-event, 22 post-event, and 51 in the current conditions) and characteristics of step–pool sequences between pre- and post-conditions. Furthermore, it proves the ongoing processes of morphological stabilization since the current step–pool sequences parameters are heading back to the pre-event values. Such results suggest clear susceptibility of step–pool to exceptional events and fast recovery of such setting during barely two years of ordinary flow conditions.