Groundwater in the Uley South basin is a vital source of water supply in the Eyre Peninsula, providing approximately 70 % of the region’s reticulated water. The groundwater resources are at risk of seawater intrusion given that the aquifer is in direct contact with the sea, and that a general lowering of hydraulic heads has occurred over the past two decades. Seawater intrusion has not been investigated thoroughly in Uley South basin; a similar situation for many of Australia’s coastal aquifers. This study develops a three-dimensional seawater intrusion model of Uley South basin using the code MODHMS. The modelling simulates for the first time the current extent of seawater in the aquifer, the temporal salinity variability, and the susceptibility of the aquifer to seawater intrusion, and as such, the model is a significant step forward beyond previous modelling attempts, providing important insights into salinity distributions and salinity mobility. While it is limited by the available information at the time, comparisons with alternative attempts at salinity measurements (e.g. an AEM survey) show a relatively close match between simulated and observed salinities; an encouraging result given well-documented uncertainties in seawater intrusion modelling. Simulations explore the effects of alternative pumping regimes, reduced recharge, and seasonality and other temporal variability effects on seawater intrusion that cannot be assessed using other methods. The impacts of pumping and recharge changes under climate variability are distinguished; both forms of aquifer stress potentially impact on heads and salinities to somewhat similar extents. The ability of the system to recover from long-term pumping is also assessed. At the basin scale, historical changes in the position of the freshwater-seawater interface are mostly localised due to the shape of the aquifer near the coastline (i.e. basement sloping towards the sea). However, the model predicts that some near-coastal piezometers may show increasing salinity trends in the future if current pumping practices continue, and in particular if recharge diminishes under climate change. A comparison between highly dynamic and averaged-stress conditions demonstrates that seasonality is a minor controlling factor in seawater intrusion trends. Aquifer recovery times exceed the periods during which the pumping stresses that induce seawater intrusion are applied. This occurs because cycles of pumping and recovery widen the transition zone between freshwater and seawater, and a large mass of salt remains in the aquifer even after an extensive recovery period.