There is a need for alternative on-site wastewater systems (OWS) that can be used in soils and on sites not suitable for conventional OWS (septic tank and gravity dispersal) while minimizing ground and surface water degradation. One method to accomplish this is to apply highly treated effluent (HTE), using a technology such as a subsurface drip irrigation system (SDIS), where effluent is dispersed uniformly to soil and the dosing frequency can be controlled. Since there are a large number of factors that can affect OWS function, the ability to evaluate these factors by using a simulation model would greatly improve our ability to design OWS that solve problems while having minimal environmental impact. This study was conducted to determine the potential to simulate HTE [recirculating media filter effluent (RMFE)] flow, soil water content and potential, and changes in soil water mass balance using HYDRUS-2D (a numerical model), in which RMFE was applied at varying rates (518, 1036, and 2071 cm3 d−1) and dosing frequencies (6, 12, and 24 doses per day) to soil columns designed to simulate a SDIS. Fecal coliform numbers were used to measure the effectiveness of these treatments. We hypothesized that fecal coliform numbers would decrease when effluent was applied in smaller (more frequent) doses. Results showed that HYDRUS-2D could be successfully used to predict RMFE flow, soil water potential and moisture content, and soil mass balance. Although dosing RMFE more frequently had no effect on fecal coliform numbers at the two lowest application rates (518 and 1036 cm3 d−1), there was a significant decrease in fecal coliforms as dosing frequency increased at the highest rate of application (2071 cm3 d−1).