In Small Island Developing States (SIDS), water pollution is not monitored or assessed frequently enough to fully understand the processes, impacts of water quality issues and what solutions are available This study investigated flushing time in Erakor lagoon and Port Vila Bay, Vanuatu using a numerical model developed in Delft3D. Microbial contamination by Escherichia coli was detected in multiple locations in the lagoon system with counts exceeding thresholds related to human health concerns. Modelling demonstrated a poor flushing time overall with a further decrease as the influence of waves and wind increased, especially in Vila Bay. Sea level rise resulted in an increase in flushing time downstream of the lagoon near the open sea, while with a decrease upstream and in Vila Bay. Based on these results, we recommend long-term continuous monitoring and identification of higher risks areas to prioritise decisions around wastewater management.