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Crete is a Mediterranean, karst-dominated island, characterized by long drought periods. The Karst-SWAT model, combined with 11 climate change scenarios, was run to assess climate change impacts on the island under two set-ups, both using the auto-irrigation function of the model: (1) with water drawn from the shallow or deep aquifer, and (2) with irrigated water derived from an unlimited outside source. The first set-up provided insight into the fluctuation of future irrigation needs, and when compared to the second set-up, enabled quantification of the future water deficit. The Water Exploitation Index was used to describe the spatial variability of future water stress on Crete. A decrease in both surface and karstic spring flows is foreseen, especially after 2060 (24.2 and 16.5%, respectively). Simulated irrigation water demand and water deficit show continuous increase throughout the projection period (2020-2098).