Coral reefs are highly diverse ecosystems that provide food, income, and coastal protection for hundreds of millions of coastal dwellers. They are found in tropical and semi tropical areas spread throughout South-east Asia, the Caribbean, the Indonesian archipelago, on Australian coasts and in the Pacific islands. Coral reefs are subject to both anthropogenic and natural threats such as biological perturbations, floods, outflows carrying pollutants from land, runoff sediment, sewage, oil wastes, mining and quarrying processes, fisheries, tourism and coastal urbanization. The period for which these pollutants stay within the lagoon depends on the residence time. The longer a pollutant stays in the lagoon before being flushed away, the more destructive it will be to the lagoon and coral reef ecosystem. Residence time is probably influenced by many factors. This study established two numerical models, a simple model and the Delft3D model, of a lagoon fringed by coral reefs with tides as the boundary conditions. The study compares the simple and Delft3D model. Then a sensitivity analysis is made of several important parameters such as tides, coral reef depth, inlet geometry and lagoon geometry.