The water resources of the atolls of the Republic of the Maldives are under continual threat from climatic and anthropogenic stresses, such as changing rainfall patterns, sea-level rise, and contamination from human activities and climatic events. Groundwater, a historically important resource of the island communities of the Maldives, is particularly affected due to the fragile nature of the freshwater lens on small atoll islands. In this study the dynamics of the freshwater lens are simulated during an extended (1998-2011) time period to determine the fluctuation of lens thickness of islands of the Maldives in response to annual and long-term changes in rainfall. Particularly, maximum and minimum lens thickness during the simulation period are assessed, as well as the occurrence of general trends, either decreasing or increasing, in lens thickness. Simulations are performed for a variety of island sizes, corresponding to the range of sizes of the islands of the Maldives, and for the various climatic regions of the Maldives. Results indicate that many of the atoll islands are expected to have a measurable freshwater lens during the majority of a long-term climatic period, although significant decreases in thickness can occur during the months of the dry season, with complete depletion occurring for small islands. Of particular note is the observation of a general decrease in lens thickness, approximately 2-4 cm/yr, over the 14-year period for the northern regions of the Maldives. If continued at current rates, these trends can have a significant impact on groundwater resources for the Maldives. Results imply that fresh groundwater, if properly protected from land surface-derived contamination and over-pumping and associated salinization, can be a valuable source of water for the Maldives, particularly for the larger islands. Overall, results provide water resource managers and government officials with valuable data for consideration in water security measures.