A modelling study of the hydrodynamics and spreading of wastewater from existing and future outfalls in the Bosphorus region has been conducted applying a 3-Dimensional model. The modelling is based on SYSTEM 3, which is a general modelling system for baroclinic flow simulating unsteady currents, waterlevels, salinity and temperature within the model area. The model set-up covers the Black Sea-Bosphorus-Marmara Sea junction area. The set-up is calibrated by data from a dedicated field program and previous field experience. The model is designed to describe the characteristic features of the flow in the junction area such as the effects of variations in waterlevel differences between the Sea of Marmara and the Black Sea on the important two-layer structure in the strait and the flow fields generated by the upper layer jet in the Bosphorus-Marmara junction. This model has been applied for evaluation of disposal of wastewater and for the subsequent water quality studies. The general use of a baroclinic 3-D hydrodynamic model to simulate disposal of wastewater is discussed. Examples of the application of the model of the junction area to evaluate the different strategies for disposal of wastewater are presented.