The forests and woodlands of the Prairie Peninsula region in the Midwestern USA have been heavily impacted by human influences over the past ∼150 years. Current composition, structure, and dynamics in forest communities across the region lie outside the historical range of variability. However, areas along major waterways were afforded greater fire protection historically than the landscape as a whole (and are common locations for modern natural areas), and historical and modern conditions may be more analogous in these locations. This study assessed composition and structure of woodlands in a series of natural areas along the Des Plaines River in Lake County, Illinois, and related current conditions to historical baselines for the locality and region. Modern composition and structure in even these fire-protected habitats appear to lie outside the historical range of variability. High canopy cover, stem density, and dominance by sugar maple (Acer saccharum Marsh.) and European buckthorn (Rhamnus cathartica L.) are especially inconsistent with historical conditions. Current structure suggests a continued trajectory toward homogenized, closed-canopy ecosystems with increased dominance by mesophytic and invasive species and decreased importance of historically-dominant oak (Quercus spp.) species. Community-specific management strategies focused on modifying canopy structure and composition will be necessary to shift these communities toward conditions of increased light availability, structural complexity, and biological diversity. Strategies to achieve these goals are currently not well established, especially those that could be applied in urban natural areas. Implementation of multiple approaches in an adaptive management framework would aid in developing best management practices for wooded ecosystems in the region.