A two-stage anoxic transformation process, involving growth of biomass utilizing two types of different electron acceptors, namely nitrate and nitrite, has been observed. The present water quality modules established for sewer processes cannot account for the two-stage process. This paper outlines the development of a model concept that enables the two-stage anoxic transformation process to be simulated. The proposed model is formulated in a matrix form that is similar to the Activated Sludge Models and Sewer Process Model matrices. The model was successfully applied to simulate changes in nitrate and nitrite concentrations during anoxic transformations in the bulkwater phase of municipal wastewater.