Characteristics of wastewater vary during transportation through sewer systems as a result of a number of processes. Under aerobic conditions, in long sewer systems, the reduction of the BOD or COD may be similar to the reduction obtained in conventional primary settling tanks. The mathematical model that was developed is based on a number of different existing models: the ASM n. 1 and ASM n. 2 models, the AEROSEPT model and the WATS model. The model also includes a prediction of reaeration at falls. The module of the anoxic conditions was adapted from the ASM n. 2 model. This module is a first attempt to model the degradation of organic matter in sewer systems under anoxic conditions. The mathematical model was applied to the Costa do Estoril intercepting sewer, and the obtained results are discussed taken into account the experimental data that was collected during a three-month period. Average removals of dissolved COD over 20% have been obtained. In the paper special emphasis is given to the importance of the performance of the Costa do Estoril sewer system as a biological reactor.