Sediments in Sydney estuary (Australia) and soils of the catchment are highly enriched in copper (Cu), lead (Pb) and zinc (Zn) and these metals are accumulating in tissue of estuarine fauna. To reduce contamination levels, especially in the tissue of bivalve filter-feeders, it is necessary to understand the processes linking source, fate and effects of metals in these environments. It was the aim of the current work to identify key mechanisms controlling bioaccumulation in shellfish inhabiting this estuary by combining the results of existing individual models and monitoring data (oyster soft-tissue concentrations) describing various parts of this system into a single source-fate-effects model. Of the existing models, an atmospheric model (TAPM) showed that vehicle emissions were the major contributor of metals to catchment soils while stormwater modelling indicated that the average annual discharge from Sydney estuary catchment ranged 215,300 - 372,000 ML with associated loadings of 60,400, 30.5, 49.0 and 89.2 tonnes for total suspended solids (TSS), Cu, Pb and Zn, respectively. A verified hydrodynamic model investigated estuarine response to catchment rainfall and showed that fresh-water plumes generated during high-rainfall events broke down within the estuary and that minimal (<1%) associated contaminants exited the estuary to the ocean, whereas TSS and pollutants delivered during low-rainfall were deposited close to discharge points and were trapped within the estuary. Oyster (Saccostrea glomerata) tissue was highly enriched in these metals, however there was no significant relationship with bottom sediment metal concentrations. The integrated model used here comprised a process-based framework describing the water and sediment balance coupled to a chemical (Cu) speciation model and an oyster bioaccumulation model. This integrated model is not spatially explicit on the horizontal plan but consists of two vertical components (aqueous layer and sediment). Early results of the source-fate-effects modelling indicate that the increase in dissolved and particulate organic ligands associated with a stormwater event entering the system appears unable to compensate for the concomitant increase in aqueous Cu and that the excess may be associated with dissolved inorganic ligands after the organic complexation sites have been exhausted. Modelling provides evidence that mechanisms driving pollution in the estuary are sensitive to catchment loading rates, which may result in highly variable soft-tissue Cu concentration in oysters.