The economy of Apulia Region largely depends on agriculture but the scarce water resources are the main factor threatening the sustainable production of this sector. This paper describes a geographical information system (GIS) based water balance tool that integrates maps of crops, climate and soil parameters with various scenarios of cropping pattern and farming practice changes. The aim is to assess the implication of these scenarios on the spatial and volumetric water needs of the region's irrigated agriculture. The total net volumetric irrigation needs, under current land use and full irrigation practices, were estimated on an average year to be 973 million m3. The deficit irrigation practices currently used in Capitanata water districts can save a volume of 302 million m3 if they are extrapolated over the entire region. Based on the Common Agricultural Policy (CAP), a replacement of 30% of the actual tomato areas in Foggia Province with sunflowers (energy crop) or durum wheat (rainfed crop) has potential water saving of 9 million m3 and 67 million m3, respectively. An additional 103 million m3 of water saving may be obtained through modernisation of the vineyards' growing practices. Findings of this paper could be used to address the agricultural policies towards a sustainable use of the scarce fresh water.