A model is presented for simulating the transport of toxic pollutants in rivers, estuaries and seas. Such transport strongly depends on the presence of suspended sediment, which is known to be an important carrier of sorbed chemicals. Hence, the movement of these contaminants can only be predicted if the movements of sediments is well understood, which also necessitates a detailed understanding of the hydrodynamic processes. Consequently, the developed model consists of different submodels for simulation of water movement, salt transport, suspended sediment transport, and transport of sorbing toxic pollutants. The model is applied to the river Scheldt (Belgium), the Scheldt estuary (The Netherlands), and the sea along the Belgian coast. Simulation results are presented for several heavy metals and organic micropollutants, as PCB, proving the importance of paniculate matter. In particular, it is shown that sorbing chemicals tend to accumulate in the estuarine sediments, while only small amounts are reaching the sea. In addition, it is found that the mobility of heavy metals is strongly influenced by salinity, and that the mobility of organic pollutants depends upon complexation with dissolved organic matter.