Paleoecological reconstructions provide valuable insights into the impacts of environmental change on key functions of wetland ecosystems. Here, we integrate biological and sedimentological proxies to provide a baseline of vegetation and hydrological change since the Middle Holocene at a riparian marsh, with the goal of informing wetland restoration within a regional biodiversity hotspot in the Great Lakes coastal zone. Four stages of wetland development are identified, reflecting the combined impacts of Lake Erie fluctuations, fluvial processes, regional paleoclimate, and anthropogenic influence. Wetland establishment took place ∼6000 cal yr BP during a Lake Erie high stand, and pollen assemblages indicate that the site was initially a forested wetland. Subsequently, water levels remained elevated as a transition to an emergent marsh with silty, organic-rich sediments took place ∼5300 cal yr BP. Once water levels stabilized in the Late Holocene, a thicket swamp established in sandier sediments, suggesting closer proximity to the meandering channel. The intensification of European settlement from 1850 CE marked a major transition, resulting from disturbances caused by land clearance and hydrological alterations, including higher rates of sediment accretion, novel diatom communities, and increases in herbaceous vegetation. These paleoecological records demonstrate the importance of considering whole-watershed measures in restoration planning, including controls on mineral sediment influxes, maintenance of local water tables, and management of invasive species producing high biomass.