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The Thames Estuary (UK) is an industrialized, macrotidal ecosystem characterized by a long history of metal pollution. Nevertheless, a holistic understanding of the metal fate is still missing. This study aims at identifying the main environmental mechanisms affecting metal behaviour in the Thames Estuary using copper and zinc as representative examples. A suite of multivariate statistical analyses performed on data from long-term monitoring of metal distribution in the estuary indicated that total metal concentrations are primarily correlated with suspended solids, being thus indirectly influenced by the interaction between freshwater discharge and the tide. These data were used to set up a three-dimensional hydrodynamic and water quality model to simulate the transport of sediments and metals within the estuary. Model results ratify that high metal concentrations might occur in the central part of the estuary as consequence of fine sediment resuspension. Such an effect of the hydrodynamics is highlighted by the differences between months characterized by low or high river discharge as well as neap or spring tide. We discuss the physical mechanisms of such transport processes and their direct implication for the management of sediment and metal contamination in estuarine areas especially in terms of long-term analysis. Developing a model able to assess future trends helps in planning the correct strategies for recovery and maintenance. Further research is needed to improve the accuracy of models of this kind as well as to investigate the potential effects of climate change for this and other similar systems.