The growing trend towards urban regeneration, particularly around water bodies, has made it increasingly important to predict the quality of urban waters. Furthermore, concern regarding hydro-environmental pollution has resulted in a marked increase in the development of computer models to assist in environmental impact assessment studies. Details are given of models used for flow and water quality indicator predictions in coastal and inland hydraulic basins, together with the limitations and restrictions of both physical and numerical models. Such models are now used routinely by non-specialist engineers and scientists to assist in the planning and design of water quality related studies. The paper then goes on to describe the development and application of a refined three-dimensional layer-integrated hydro-environmental model to predict water elevations, layer-averaged velocity components and the distribution of water quality indicators within Cardiff Bay, Wales. The model includes the prediction of flushing through the bay of spillages from combined sewer overflows or riverine inputs. Details are also given of field measurements taken for a range of variables used to describe the role of environmental factors and the interaction of various parameters in predicting the survival rates of bacteria in the numerical model.