Rapid infiltration basin systems (RIBS) are used for the application of treated wastewater to soil for wastewater disposal. To ensure sufficient additional wastewater treatment, U.S. regulations require a minimum separation distance between the infiltration basin and groundwater. Analytical and numerical models that predict groundwater mounding beneath basins have assumed a uniform specified flux boundary condition across the basin. In many systems, however, the basins are only partially flooded, with overland flow and soil infiltration controlling the extent of basin inundation. The iTOUGH2 computer code was modified to describe the coupled surface–subsurface flow in RIBS. After testing the model with published laboratory and field data, simulations were used to estimate groundwater mounding beneath RIBS for four hydraulic loading rates and two flooding periods in two representative soils. Because of interest in nitrate (NO3−) removal beneath RIBS, a simplified approach using a domain-average denitrification reduction factor, Fs, was used to assess the impact of pore water saturation on denitrification. Simulations using the conventional specified flux boundary condition underpredicted groundwater mounding by as much as a factor of 25 in loamy sand and a factor of 6 in sand. The impact of the basin boundary condition on Fs was less significant, with Fs reduced by up to 50% if the specified flux boundary condition was used. Thus, ignoring overland flow underpredicts denitrification and groundwater mounding for the cases studied here. For a fixed amount of wastewater discharged during a weekly flooding–drying cycle, simulations indicate that longer flooding periods result in less groundwater mounding but a reduction in denitrification.