Some of the most biologically diverse coastal wetlands and estuaries are found along the Great Lakes, but the spatial extent and timing of river-related inundation and sedimentation vary greatly among natural and altered systems. We used hydrologic data, geomorphic change detection, and satellite imagery to study inundation and sedimentation patterns in the naturally dynamic estuary of the Bad River (Mashkiiziibii) that flows into Lake Superior (Anishinaabeg-gichigami), and the Kakagon River (Ogaakaagaang-ziibii) that flows into a sheltered bay (Chi-Kaamigong). In 2016, an extreme summer flood (annual exceedance probability < 0.2 %) caused total inundation of the 46-km² estuary. Floods from the sediment-rich Bad River, with an annual exceedance probability of ≤ 50 %, have overflowed into the upper wetlands and channels of the Kakagon River about 60 times over the last 75 years, including 20 floods during the most recent 10-year wet period. Sedimentation patterns were associated with proximity to river channels, shoreline erosion, and wind action. Early winter ice-up coupled with a storm surge and an early spring snowmelt into the iced-over bay changed inundation duration and sedimentation patterns. Climate-change projections for more intense rainfall and warmer temperatures will likely cause more frequent flooding and sedimentation; however, patterns may differ depending on the timing of the floods relative to storm surges and ice formation, or other factors. The approach of integrating readily available data helped give a broader temporal and spatial context to the possible causes for inundation and sedimentation, some expected and others not, in natural and restored estuaries of the Great Lakes.