Restoration of disturbed wetland systems is an important component of wetland mitigation, yet uncertainty remains about how hydrologic processes affect biologic processes and wetlands patterns. To design more effective restoration strategies and re-establish native plant communities in disturbed wetlands, it is imperative to understand undisturbed systems. A site within Cherokee Marsh located in Madison, Wisconsin, USA, contains a relatively undisturbed area of wetland consisting of plant communities common within the prairie landscape including a fen, sedge meadow, and shallow marsh. These distinct communities are found within an area of minimal topographic relief, yet transitions from one community to the next occur over short distances. This study sought to characterize the geologic, hydrologic, and chemical gradients associated with these shifts in vegetation to gain insight into the factors controlling the spatial differences in dominant plant species, which could be critical for restoration success. Vegetation analyses revealed a transition of dominant sedge species, which appeared to correspond to changes in hydrology from a ground-water dominated to a surface-water dominated system (as determined by water isotopes). Along the same vegetation transect, subsurface coring results show a heterogeneous composition of peat and till with lateral and vertical variations in stratigraphy, which relates to variability in ground-water discharge as evidenced by hydroperiods and stable isotope composition. Applications of this type of approach throughout the glaciated terrains of the midwestern and northeastern United States and Canada can improve future wetland restoration and management.