The biological and geochemical processes in soil such as organic matter mineralization, microbiological activity, and plant alimentation can be accurately assessed and modeled only with the knowledge of the thermodynamic status of the soil medium where these processes take place. However, current soil water models do not define and characterize the soil structure or the thermodynamic state of the soil water interacting with this structure. This article presents a new paradigm in characterizing and modeling the organized soil medium and the physical properties resulting from this organization. It describes a framework of the modeling approach as a contribution to the General Systems theory. The basic concept of Representative Elementary Volume (REV) in soil physics and hydrology was transformed into the concept of Structure Representative Volume (SREV) which takes into account the hierarchical organization of the structured soil medium. The pedostructure is defined as the SREV of the soil medium and this concept is at the basis of the new paradigm including variables, equations, parameters, and units in soil physics, in a similar way that the REV is at the basis of the continuous porous media mechanics applied to soils. The paradigm allows for a thermodynamic characterization of the structured soil medium with respect to soil water content then bridging the gap between pedology and soil physics. We show that the two points of view (REV and SREV) are complementary and must be used in the scaling of information. This approach leads to a new dimension in soil–water properties characterization that ensures a physically based modeling of processes in soil and the transfer of information from the physical scale of processes (pedostructure or laboratory measurements scale) to the application scale of the other disciplines (modeling and mapping scale).