The Jamuna is a major braided river of Bangladesh and poses enormous challenges related to flooding, erosion, and sedimentation. Effective river management requires an understanding of the Jamuna’s sediment transport dynamics and channel morphology. Yet, developing that understanding is hindered by a lack of topographic data for the river corridor. In this study, the waterline method was applied to a 65 km reach of the Jamuna to derive river channel and floodplain topography above the low water level. The analysis relies on surface water detection from Sentinel-1 and Sentinel-2 data, along with in-situ water level observations, to generate river-floodplain DEMs for the years 2016–2019. Morphologic change was assessed through DEMs of difference for sequential years and for the overall study period. A quantitative uncertainty analysis was conducted to characterize errors in the waterline DEMs, vertical change detection, and gross and net volumetric changes. The results indicate that gross annual erosion and accretion volumes have a similar order of magnitude to contemporary estimates of the river’s sediment influx. The study highlights that localized and reach-scale lateral exchange is a key component of the overall sediment budget. Finally, the uncertainty analysis framework provides insight and recommendations for how errors can be assessed and reduced in future waterline applications.