Multi-temporal repeat monitoring of flood-vulnerable rivers is crucial due to rapid alteration of morphological properties of in-channel landforms. Besides, the characteristics of the river crossing bridges may deteriorate due to flood induced scouring around bridge piles or due to flood loads. Thus, in this study high-resolution topography of the study region was acquired during two consecutive years by unmanned aerial vehicle (UAV) based surveys using Structure-from-Motion (SfM) processing. Following the extraction of digital elevation models (DEM), repeat data that were obtained at each UAV survey were compared using Geomorphic Change Detection (GCD) to calculate volumes of deposition and erosion via DEM of difference (DoD) algorithm. Thus, detailed high-resolution maps of the river channels can be rapidly and efficiently generated by low cost UAV based measurement methods in order for continuous tracking of stream channel morphology for the rivers sensitive to floods.