Wetland restoration projects attempt to recreate the hydrology found in natural wetlands, but little is known of the water budgets associated with wetlands in their natural state. The objective of this study was to compute the water budgets of three natural Carolina bay wetlands in Bladen County, North Carolina, USA. DRAINMOD models of various locations in the bays were calibrated with measured water table depths over a 2-yr period using inputs of rainfall, air temperature, and soil physical properties. The models were successful in simulating water table depths at all well locations during the calibration period with average absolute deviations between simulated and measured water table depths of approximately 4 cm. Measured and simulated data revealed very shallow (< 0.1 m) water table depths at all of the bays. Groundwater inflow was a significant component of the water balance at locations near the perimeters of the bays, ranging from 3%–26% of the total water input for these sites during the study period. A semi-confined aquifer below one of the bays was likely the source of groundwater inflow for that bay. Meanwhile, locations near the centers of the bays did not have groundwater inflow as an input to their water budgets. Groundwater outflow for the centers of the bays ranged from 2%–21% of rainfall. Areas near the perimeters of the bays were recharge, discharge, or flow-through wetlands depending on hydrologic conditions at the sites. Areas near the centers of the bays exhibited characteristics of recharge wetlands only. These results were consistent across the three Carolina bays studied, and can be used to better understand the hydrology of natural Carolina bays, improving the success of restoration projects of similar sites.