Small islands rely heavily on groundwater resources in addition to rainwater as the source of freshwater since surface water bodies are often absent. The groundwater resources are vulnerable to sea level rise, coastal flooding, saltwater intrusion, irregular pattern of precipitation resulting in long droughts and flash floods. Increase in population increases the demand for the limited groundwater resources, thus aggravating the problem. In this study, the effects of climate change on Tongatapu Island, Kingdom of Tonga, a small island in Pacific Ocean, are investigated using a sharp interface transient groundwater flow model. Twenty nine downscaled General Circulation Model(GCM) predictions are input to a water balance model to estimate the groundwater recharge. The temporal variation in recharge is predicted over the period of 2010 to 2099. A set of GCM models are selected to represent the ensemble of 29 models based on cumulative recharge at the end of the century. This set of GCM model predictions are then used to simulate a total of six climate scenarios, three each (2010-2039, 2040-2069, and 2070-2099) under RCP 4.5 and RCP 8.5. The impacts of predicted climate change on groundwater resources is evaluated in terms of freshwater volume changes and saltwater ratios in pumping wells compared to present conditions. Though the cumulative recharge at the end of the century indicates a wetter climate compared to the present conditions the large variability in rainfall pattern results in frequent periods of groundwater drought leading to saltwater intrusion in pumping wells. Thus for sustaining the limited groundwater resources in small islands, implementation of timely assessment and management practices are of utmost importance.