On-site wastewater treatment systems (OWS) are a common means of wastewater treatment in coastal North Carolina, where the soils are sandy and groundwater is relatively close to the surface (<5 m). Wastewater contains elevated concentrations of pathogenic microorganisms that can contaminate groundwater and surface water if OWS are not operating efficiently and distributing wastewater equally to all drainfield trenches. The objectives of this study were to compare the distribution of fecal indicator bacteria (FIB) in groundwater beneath a large low-pressure pipe (LPP) OWS and a large pump to distribution box system, and to determine the effectiveness of the systems in reducing FIB including total coliform, E. coli, and enterococci. Monitoring wells were installed at the fronts and ends of the drainfields for sample collection. Groundwater beneath the LPP had a more homogeneous spatial distribution of E. coli and enterococci concentrations and the specific conductivity of groundwater was also more uniform relative to groundwater beneath the distribution box system. Both systems were effective (>99%) at reducing FIB concentrations before discharge to groundwater. Results indicate that the LPP did enhance the distribution of FIB in groundwater beneath the drainfield area relative to the pump to distribution box system. Although the LPP system had a vadose zone over 2 m thinner than the pump to distribution box system, FIB treatment was similar. Enterococci was the most resilient FIB of the three tested.