Clayey subsurface strata in precipitation-driven wetlands act as aquitards that retain water and can affect wetland hydrology. If the aquitard layers have been cut through by drainage ditches, then restoring wetland hydrology to such sites may be more difficult because of the need to fill ditches completely with low hydraulic conductivity material. Ground penetrating radar (GPR) surveys were conducted to determine the depth and continuity of shallow clay layers and identify those that have been pierced by drainage ditches at Juniper Bay, a 300-ha drained Carolina bay in North Carolina, USA that will be restored. Carolina bays are a wetland type that occur as numerous, shallow, oval-shaped depressions along the Atlantic Coastal Plain. The GPR interpretations found that moderately fine-textured (clay loam, sandy clay loam, silty clay loam) and fine-textured (sandy clay, silty clay, clay) aquitards underlay coarser-textured horizons in most of the bay at an average depth of 1.6 m. Extensive ground truthing showed that, on average, GPR predicted the depth to these aquitards to within 16% of their actual depth. An atypical GPR reflection in the southeast sector of the bay was interpreted as a fluvial deposit without aquitards until a depth of 3 to 5 m. This area may require different restoration strategies than the rest of the bay. By comparing the depths of aquitards and drainage ditches, several areas were identified as likely locations of ditch-induced aquitard discontinuity that may require filling or lining of suspect ditches to prevent potential water losses if there are downward hydraulic gradients. Cost estimates by two professional firms indicated that GPR could provide large volumes of data with cost and time efficiency. GPR surveys are proposed as a useful tool for characterizing potential wetland restoration sites on the Atlantic Coastal Plain and other regions with similar soils.