•A high resolution coupled circulation–wave–sediment transport model is implemented.•The model is efficient in terms of computational time taking advantage of it parallelization.•An alternative coupling procedure is suggested for sensitivity analyses and calibration.•Wave induced stress are essential to represent the main re-suspension events.•SSC inside the bay controlled by advection of sediment from the near coastal area. Modelling the hydrodynamics and fine-sediment dynamics in estuarine environments is important for coastal engineering design and environmental assessment. This paper presents the application of a coupled wave–current–sediment transport model to a complex estuarine system with high spatial resolution in a harbour area. The case study was the Río de la Plata, with a focus on the Montevideo Bay area. We used a bidimensional depth-averaged approach, and the sediment transport modelling focused on fine cohesive sediments. The model considers realistic forcings, allows for the simulation of complex geometries such as those present in harbour basins and is capable of providing long-term environmental simulations (on the order of several years) within reasonable computational times. The model results are in good agreement with the measured data and satisfactorily represent the main features of the flow and sediment dynamics of the Río de la Plata. The effect of the internal coupling on the hydrodynamic results is analysed, and the computational times with various coupling alternatives are discussed. The dynamics of fine sediment in Montevideo Bay were analysed based on the model results. The current-induced bottom shear stress results are relevant for representing the permanent suspended sediment concentrations, whereas the wave-induced bottom shear stress is fundamental for reproducing the main resuspension events during storm conditions. The suspended fine-sediment dynamics in the estuary are strongly controlled by the sediment exchange between the bed and water column, whereas inside Montevideo Bay, the dynamics are controlled mainly by advection of sediment originating from the nearby coastal area.