Forest ecosystems in eastern North America were in flux over the last several thousand years, well before Euro-American land clearance and the 20th-century onset of anthropogenic climate change. However, the magnitude and uncertainty of prehistoric vegetation change have been difficult to quantify because of the multiple ecological, dispersal, and sedimentary processes that govern the relationship between forest composition and fossil pollen assemblages. Here we extend STEPPS, a Bayesian hierarchical spatio-temporal pollen-vegetation model, to estimate changes in forest composition in the upper Midwestern United States from about 2000 to 200 years ago. Using this approach, we identify areas of statistically and ecologically significant change. Between 2000 and 200 years ago, forest composition significantly changed across broad regions of north-central Wisconsin and Minnesota. Rates of compositional change varied spatially, and can be linked to previously reported events. The single largest change is the infilling of Tsuga canadensis in northern Wisconsin over the past 2000 years. Despite this range in-filling, the range limit of T. canadensis was largely stable, with modest expansion westward. The regional ecotone between temperate hardwood forests and northern mixed hardwood/conifer forests shifted southwestward by 15-20 km in Minnesota and Northwestern Wisconsin. Fraxinus, Ulmus, and other mesic hardwoods expanded in the Big Woods region of southern Minnesota. However, some areas showed no significant change, suggesting high complexity in the spatiotemporal patterns of past forest dynamics. The increasing density of paleoecological data networks and advances in statistical modeling approaches now enables the confident detection of subtle but significant changes in forest composition over the last 2000 years.