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The subject of this article is the dynamics of water in a soil pedostructure sample whose internal environment is subjected to a potential gradient created by the departure of water through surface evaporation. This work refers entirely to the results and conclusions of a fundamental theoretical study focused on the molecular thermodynamic equilibrium of the two aqueous phases of the soil pedostructure. The new concepts and descriptive variables of the hydro-thermodynamic equilibrium state of the soil medium, which have been established at the molecular level of the fluid phases of the pedostructure (water and air) in a previous article, are recalled here in the systemic paradigm of hydrostructural pedology. They allow access to the molecular description of water migration in the soil pedostructure and go beyond the classical mono-scale description of soil water dynamics. We have specially studied and physically defined the flux of water in the soil pedostructure at its three levels of scale of organization: the Eulerian flux at macroscopic level of the total section of the pedostructure sample, the real flux of the two aqueous phases of the pedostructure through the inter primary-aggregates space; and the molecular flux of the mobile aqueous phase in the inter primary-aggregates space. The continuity equation can be written for each of these fluxes at the three scale levels and it is that defines the space/time ratio we need to establish the thermodynamic equation of the water conductivity. The experimental results show a perfect agreement with the theory, validating at the same time the systemic approach which was the framework.