Background and Objective: Agricultural crops require high volumes of water and fertilizers. Nowadays, water resources are scarce, also for climate changes, and fertiliser production requires large amounts of non-renewable resources such as phosphorus. The TOMRES project (Horizon 2020, n. 727929) involved 25 partners from 10 European countries with the aim of increasing tomato tolerance to the combination of water and nutritional stress. Sustainable management strategies suitable for water and nutrients absorption from soil were tested and optimised, including fertilisation, irrigation techniques, symbiotic microorganisms and biostimulants use. With the purpose of assessing the effects on Public Health, the evaluation of the hygiene and sanitary impact of the new cultivation method was investigated. Methods: Microbiological indicators and pathogens, ecotoxicological indicators, pesticides and heavy metals contamination were analysed on soil samples in relation to the agronomic techniques applied in the project trials. To evaluate the hygiene and sanitary impact a statistical comparison of the Results obtained in soil samples between pre- and post-cultivation (t-test) and among the different cultivation strategies applied in each trial (ANOVA) was carried out. Results: The overall Results showed that the reduction of water and fertiliser use leads to a reduction of bioavailable heavy metals, microbiological contamination and ecotoxicity. However, the results underlined that the use of these sustainable agronomic practices should be managed with particular attention in areas where there may be over-fertilization due to previous agricultural activities because of the risk of toxic substances mobilization in the soil. Conclusions: The agricultural practices evaluated in the TOMRES project are promising as they limit heavy metals mobility, microbiological contamination and ecotoxicity. So, resilient tomato cultivars could grow using new crop management techniques with a reduction of water and nutrient consumption that is a fundamental goal for linking the growth of the world population with climate changes.