<p>Freshwater resources are scarce on islands surrounded by seawater, where groundwater lenses are often the only sources of fresh water. These resources are highly sensitive to climate variability and human activities, requiring specialized management approaches. Here, groundwater flow models that account for climate and parameter uncertainty are used to guide groundwater resource management on the Magdalen Islands (Quebec, Canada). An island-wide groundwater flow model was developed for four islands of the archipelago using MODFLOW-2005 and the sharp interface seawater intrusion package SWI2, driven by a spatially distributed SWB2 recharge model. Parameter estimation was then conducted using PEST_HP, producing island-wide maps of the freshwater lenses and water budgets. Transient simulations were run to determine the percent rise of the freshwater–seawater interface below pumping wells relative to the onset of pumping. The model was then combined with PESTPP-OPT and climate change projections to conduct pumping optimization under climate and parameter uncertainty, and with MODPATH to delineate zones for groundwater protection. The modeling results indicate that groundwater resources will be sufficient to meet the future water demand on the islands as projected through 2050. While some wellfields can provide more fresh water, others cannot, and certain wells may be at risk of saltwater intrusion in the future. Climate change is unlikely to impact overall groundwater resource availability, but it will reduce the volume of freshwater that can be withdrawn from existing wellfields. The scripted, open-source modeling approach used here can be applied to similar environments to address common management challenges encountered in island aquifer settings.</p>