The physical properties of soil depend upon soil structure which is defined by the size, shape and arrangement of ultimate particles, aggregates of particles, and voids. Properties of the soil change as the amount of water occupying the voids varies, and also because of structural change associated with management and with biological activity. Traditionally, the physical behaviour of this system has been intensively studied in terms of macroscopically measurable properties considered to be “characteristic” of substantial volumes of soil, with the principal aim being the description, prediction, and management at the field scale. In comparison with this effort, study at the scale of the soil pore, or sequence of pores, has been modest. Yet this is the appropriate scale to use when describing the environment of many soil organisms. This paper re-examines basic issues relating to the physical environment affecting soil-borne organisms. It reappraises the relevance of “macroscopic” variables, in relation to experience and behaviour of organisms, comments on methods used to define them, and suggests that important physical variables must be defined at the scale of the particular organism. Within this framework, it is suggested that local “thermodynamic equilibrium” is generally the rule, so that the thermodynamic potential of an entity (such as water), and its measurement, may transcend scale. The distribution of water in soil at a defined water potential is, however, scale-dependent, and at the level of the pore can only be inferred from simple physical models applied to the local geometry of the soil surfaces. This issue is examined in some detail, because the amount and distribution of soil water is important not only in relation to water availability, but also because of the profound effect soil water content has on organism movement, soil strength, thermal properties of soil, and gas transfer.