The aim of this paper is to evaluate the water footprints (WFs) of all the main crops on Rhodes island at a municipal unit (MU) scale, as well as for the area of the island as a whole. WF estimations are made with a distinction of rainfed and irrigated crops, using CROPWAT 8.0. Rainfed crops and the drip irrigation method are predominant in the study area, which faces water scarcity issues. Furthermore, a reduction factor in plant coefficients is introduced, to adapt to the drip irrigation technique. From the findings obtained, useful conclusions are drawn regarding the most water-demanding crops, but also the type of their WF component (blue/green/gray). In all categories of crops, there are large fluctuations across MUs, mainly due to the different yields. Higher WF values occur for rainfed and irrigated olives, which constitute the predominant crop, followed by hard and soft wheat. WF is a useful indicator identifying which crops require improvement or restructuring in a study area, and quantifies the exact volumes of water, which is a useful element in the formulation of agricultural policy in the context of sustainable water resources management.