Permeable denitrifying barriers with injected vegetable oil have shown promise for removing nitrate from contaminated groundwater. The carbon/nitrogen (C/N) module in Root Zone Water Quality Model (RZWQM) has been improved and modularized for easy implementation. This module was used to simulate the denitrification process in the barriers as affected by vegetable oil content and phosphate additives. The denitrification process was divided into two sub-processes in the module: nitrate to nitrite and nitrite to N2O and N2. Each sub-process was simulated as a first-order kinetics that was a function of available substrates and denitrifier population. The growth of denitrifier population was controlled by available organic carbon and available nitrogen and phosphorus to maintain appropriate C:N and C:P ratios for microbial biomass. The new denitrification module was coupled to the convective-dispersive equations for nitrate, nitrite and phosphate transport, and was tested against a series of laboratory column studies, where saturated flow was maintained and various amounts of vegetable oils and phosphate were injected. Simulation results showed that the model correctly simulated the capacity of the columns to remove nitrate from flowing water with different amounts of oil injection. It also correctly simulated less nitrite accumulation with increasing phosphate addition.