According to the literature, biological processes in the rhizosphere could play a role in the adaptation of plants to droughts under a changing climate. A previous study has identified significantly different productivity level and fruit quality for two tomato varieties under water deficit conditions. We conducted a field study, with and without water deficit, with these two varieties to examine whether microbiological activity and exopolysaccharides concentration could affect soil hydrophysical properties. The rhizosphere soil had indeed distinct bio-chemical and hydrophysical properties between the two cultivars and between the two water-related conditions. The quantity of soil exopolysaccharide and/or nitrogenous substances, and the activity of microorganisms (fungi in particular) explains part of the soil water retention measurements. In addition, these mechanisms are significantly accentuated for the cultivar with the best productive capability under water-limited condition—i.e. with commercial yield, fruit dry matter and water use efficiency which are respectively 35%, 28%, and 31% higher for the productive cultivar.