Understanding the fresh groundwater lens (FGL) behavior and potential threat of climatic-induced seawater intrusion (SWI) are significant for the future water resources management of many small islands. In this paper, the FGL of Kish Island, an arid-region case in the Persian Gulf, Iran, is modeled using two-dimensional (2D) and three-dimensional (3D) simulations. These simulations are based on the application of SUTRA, a density-dependent groundwater numerical model. Also, the numerical model parameters are calibrated using PEST, an automated parameter estimation code. Firstly a detailed conceptualization of the FGL model is completed to understand the sensitivity of the FGL to some particular aspects of the model prior to analysis of climate change simulations. For these investigations, the FGL system is defined based on Kish Island system to accomplish the integrated comparison of features of a conceptual model that are representative of real-world systems. This is the first study which adopts such an approach. The comparison of cross-sectional simulations suggests that the two-layer properties of the Kish Island aquifer have a significant influence on the FGL while the impacts of lateral-boundary irregularities are negligible. The impacts of sea-level rise (SLR), associated land-surface inundation (LSI), and variations in recharge rate on the FGL salinization of Kish Island are investigated numerically. Variations of SLR value (1-4 m) and net recharge rate (17-24 mm/year) are considered to cover a possible range of climatic scenarios in this arid-region island. The 2D and 3D simulation results demonstrate that LSI caused by SLR and recharge rate variation impacts are more important factors in the FGL in comparison to estimated SLR impacts without LSI. It is also shown that climate change impacts on the FGL are long-term to reach a new FGL equilibrium in the case of Kish Island's aquifer system. The comparative analysis of 2D and 3D results shows that three-dimensionality is a significant factor, especially in large-scale 3D systems of small islands. The results of this study are expected to have implications for the understanding and management of the fresh groundwater resources of Kish Island and are also expected to be relevant to the study of the impact of climate change on groundwater resources on islands worldwide. (C) 2014 Elsevier B.V. All rights reserved.