The Seine estuary (France) is currently one of the world's most contaminated estuaries, due in particular to its high cadmium and lead content. Proper understanding of contaminant transfer, transformation and retention mechanisms throughout the estuary and up to the adjacent marine zone require a range of studies involving data collections, experiments, and modeling tool. A multivariable transport model (SiAM-3D) was used to simulate dissolved and particulate transport and it is applied to several calculation grids; a speciation model (MOCO) was used to select key species and obtain a schematic system representation. The coupled model for Cd and Pb was compared with field measurements. The complementary character of various tools (model applied to annual time scale, in situ measurements and experiments) allowed to explore and quantify various hypotheses on the high dissolved cadmium concentrations observed during low river flow. The target is to achieve a compromise between acceptable computing times and adequate result accuracy. Although particle and contaminant behaviour is globally well-reproduced by the coarse grid, calculation errors relating to bayward fluxes and stocks deposited inside the estuary were highlighted after comparison with the fine grid.