Vineyards represent complex Mediterranean agrosystems that deliver significant ecosystem services to society. Yet, many vine-growers still need to assimilate the importance of crop and soil management to the conservation of soil and water resources. The main objective of this study was to evaluate water use and the water balance terms in rainfed and irrigated vineyards in Italy and Portugal, respectively, in both cases aiming at the sustainability of natural resources use. The SIMDualKc model is used for both sites after calibration and validation by fitting soil water content measurements. The Italian case study focused on the impacts of inter-row conservation management in hillslope vineyards while the Portuguese case study analyzed irrigation water management under scarcity in flat vineyards. For the Italian vineyards, the model results focused on the evapotranspiration fluxes and their partition, control of surface runoff, and soil water recharge provided by the inter-row soil management using cover crops. Model results of the Portuguese case study showed the need for improving irrigation water use and the terms of water balance, namely referring to percolation and soil water evaporation. Both case studies further demonstrated the advantages of using computational tools to better cope with climate variability in the Mediterranean region and made evident the benefits of improved crop and soil management practices in counteracting land degradation and valuing the use and conservation of natural resources.