A typical onsite wastewater treatment system consists of a septic tank and a soil treatment unit to treat wastewater before it is discharged through the vadose zone to an aquifer. A tool was developed for the purpose of predicting the fate and transport of nitrogen in soil treatment units (STUMOD or Soil Treatment Unit Model). STUMOD calculates nitrogen species concentrations and the fraction of total nitrogen reaching the aquifer or a specified soil depth. Input data include parameters for hydraulics and nutrient transport and transformation. An analytical solution is used to calculate the profile of pressure based on Darcy’s equation and the relationships between suction head, unsaturated hydraulic conductivity, and soil moisture. Chemical transport is based on simplification of the advection–dispersion equation. STUMOD is relatively simple to use but accounts for important processes such as ammonium sorption, nitrification, and denitrification. STUMOD accounts for the effect of soil moisture content (a surrogate for redox conditions) on nitrification and denitrification reactions. The model has provisions to handle the influence of temperature and organic carbon content on nitrogen transformation. Model outputs, generated based on input parameters obtained from extensive literature review, were compared to a numerical model and data from laboratory tests and field sites. Both measured data and STUMOD outputs show a relatively higher removal in clayey soils compared to sandy soils. Consistent with literature data for most soils, STUMOD predicted ammonium conversion to nitrate within the first foot below the trench infiltrative surface.