This study addresses the sustainable use of water resources in the Mediterranean basin, particularly in the Southern and Eastern parts of the region, and the many problems generated by water scarcity and misuse. Water economy in the region is beset by two specific problems: high irrigation needs and changes in consumer demands (especially after population shifts from rural to urban areas and because of increasing tourism and industrialisation). The challenges presented by the water crisis are even greater because of growing populations and estimated future climatic changes in the region. The integrated management of limited water resources in the Southern and Eastern parts of the Mediterranean involves several areas of research. Those most directly related with agriculture concern improving water (and nutrient) use in agriculture through the management and breeding of irrigated and rain-fed crops. However, these fields of research address only one face of a multi-factorial equation that affects water sustainability in the region. Thus, other research fields include the design of comprehensive water policies and integrated planning, and technologies for advanced water treatment and re-use. Moreover, local problems and socio-economic aspects must be considered when addressing research issues.