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According to the IPCC 2014 report the Mediterranean region will be affected by strong climatic changes, both in terms of average temperature and of precipitations regime. This area hosts some half a billion people and the impact on food production will be severe. To implement a climate smart agriculture paradigm and a sustainable increase of agricultural productivity different approaches can be deployed. Agriculture alone consumes 70% of the entire water available on the planet, thus the observed reduction of useful rainfall and growing costs for irrigation water may severely constrain food security. In our work we focused on two typical Mediterranean crops: durum wheat, a rainfed crop, and tomato, an irrigated one. In wheat we explored the possibility of identifying genotypes resilient to water stress for future breeding aims, while in tomato we explored the possibility of using biostimulants to increase the plant capacity of using water. In order to achieve these targets, we used high throughput phenotyping (HTP). Two traits were considered: digital biovolume, a measure based on imaging techniques in the RGB domain, and Water Use Efficiency index as calculated semi-automatically on the basis of evaporation measurements resulting in a high throughput, non-destructive, non-invasive approach, as opposed to destructive and time consuming traditional methods. Our results clearly indicate that HTP is able to discriminate genotypes and biostimulant treatments that allow plants to use soil water more efficiently. In addition, these methods based on RGB quality images can easily be scaled to field phenotyping structure USVs or UAVs.