Floods often cause changes in the hydro-geomorphology of riverbeds and banks. These changes need to be closely monitored to find a balance and exchange between lateral and vertical erosion and deposition, upstream local sediment supply, and a stream’s transport capacity. Low-frequency cross-sectional field surveys cannot map hard-to-reach locations. Innovative techniques, such as small unmanned aerial vehicles (UAVs), must be employed to monitor these processes. This research compared historical data with a UAV survey and the Pix4DMapper structure-from-motion (SfM) program to assess the longitudinal, lateral, and vertical changes of Sidere Creek in the eastern Black Sea, Türkiye. Digitization was undertaken using 2011–2015–2017 Google Earth photographs, 1960s topographic maps, and 2023 orthomosaics. ArcGIS 10.6 was used to delineate the centerlines (thalweg), left/right banks, alluvial bars, active channel widths, and channel confinement layers. Channel Migration Toolbox and CloudCompare were utilized for analyzing lateral and vertical morphological changes, respectively. The active channel migrated 25.57 m during 1960–2011, 15.84 m during 2011–2015, 6.96 m during 2015–2017, and 5.79 m during 2017–2023. Left-bank channel confinement rose from 2.4% to 42% and right-bank channel confinement from 5.9% to 34.8% over 63 years. Neither stream meandering nor sinuosity index changed statistically. Active channel boundary widths varied from 149.79 m to 9.46 m, averaging 37.3 m. It can be concluded that UAV surveys can precisely measure and monitor the stream channel longitudinal, lateral, and vertical morphological changes at a lower cost and in less time than previous methods.