Russ, EmilyExcess fine sediment is one of the main pollutants contributing to water quality degradation in the upper Chesapeake Bay. Recent management efforts have focused on reducing sediment inputs within the Bay watershed to achieve water quality standards set in the Chesapeake Bay Total Maximum Daily Load (TMDL). However, the models used to develop the TMDL did not account for the evolving sediment loads to and storage in the Bay, which include reduced sediment capacity in the Conowingo Reservoir, the last reservoir on the Susquehanna River, increased shoreline protection measures, and resurgence of SAV in the upper Bay in a region known as the Susquehanna Flats. The overall goal of this dissertation is to assess the current sediment dynamics of the upper Bay and specifically evaluate the connectivity of sediment transport from the Susquehanna River through the Flats into the upper Bay. First, I evaluated sedimentation on the Susquehanna Flats over seasonal to decadal time scales using radioisotopes within the context of submersed aquatic vegetation (SAV) biomass and geomorphology. Seasonal-scale sedimentation variability was related to river discharge, sediment supply, and geometry over the SAV bed, while decadal-scale sedimentation was influenced by flood events and changes in SAV biomass abundance. Next, I analyzed sediment geochemical patterns in the upper Bay using statistical analyses. Elements associated with aluminosilicate minerals, rare earth elements, and heavy metals explained the most variability in the dataset due to changes in grain size, salinity, and anthropogenic input, respectively. A sediment-provenance analysis was performed using the sediment-geochemistry data and indicated that the Susquehanna is the dominant source of fine-grained material throughout the upper Bay. Finally, I developed an updated sediment budget through quantitative analysis of sediment sources (Susquehanna River and shoreline erosion) and sinks (Susquehanna Flats and mainstem sediment-accumulation rates). Conservation-management practices have reduced Susquehanna River sediment loads at low flows, but sediment loads at high flows have increased, consistent with a decreasing scour threshold for bottom sediments in Conowingo Reservoir as it has filled. Increases in shoreline stabilization have reduced shoreline erosion inputs.enDissertationEnvironmental scienceGeomorphologyChesapeake BaySedimentsediment budgetsediment provenancesediment-vegetation interactions