An extensive environmental study of the Tejo estuary indicated that one of the major sources of pollution in part of this estuary are the sewer discharges of Lisbon, Portugal. To assess the impact of alternative plans for pollution abatement, a model is required which can predict the extent of pollution in the system resulting from different sources. The model simulates the movement of water in the estuary and also the movement of substances which are dissolved in the water. In addition, the breakdown of these substances can be simulated. This paper discusses the formulation of the model, the model adjustment, flow fields, tide-induced residual circulations, quasi-steady state coliform distribution, coliform distribution after rainstorms, and sub-models.