Population growth, industrialisation and increasing agricultural demands have significantly stressed groundwater resources in Pacific Island countries (PICs). Climate change and sea-level rise also affect the groundwater resources in PICs. These anthropogenic and natural factors give rise to saltwater intrusion (SWI), a major growing environmental problem in the PICs. SWI is a highly non-linear process which makes it more complex to manage. However, with the help of numerical modelling, SWI can be monitored, managed and controlled. In the present study, we used an illustrative study area where the hydrogeological parameters and other boundary conditions used are similar to the PICs aquifer systems in Vanuatu. The scenarios include changing the barrier wells, injection wells, recharge, hydraulic head, hydraulic conductivity and grid size. The numerical simulation model of the study area was developed, and different scenarios were tested using SEAWAT modules. Apart from salt, we also modelled leachate and engine oil present in the investigated study area to see how it affects the freshwater wells over time. The scenario-based sensitivity analysis tests indicate that injection wells, recharge and hydraulic conductivities are highly sensitive, and with the proper modification, SWI can be managed or regulated. The sensitivity of grid size showed that the simulated results varied within the 10% range of different gird sizes. Moreover, it was also found that the rise in sea level or coastal heads by 0.3–1 m does not significantly cause further SWI encroachment in aquifers. The results from this study are very crucial in this modern era when freshwater needs in coastal areas, especially PICs, are rapidly increasing, and fresh groundwater resources are declining. The novel outcome presented in this study opens pathways for further detailed modelling and numerical studies in the field of SWI management strategy development and is, therefore, beneficial for policymakers, groundwater modellers and general scientific communities.