Soil deformation is a perpetual process in the pedosphere where besides physicochemical stresses primarily alternating hydraulic and mechanical stresses continuously re-arrange the configuration of solid particles. In this study we present a local strain analysis and changes in soil structure resulting from hydraulic and mechanical stresses based on X-ray microtomography data. Digital image reconstructions were used to quantify local structural pore space characteristics and local soil deformation by 3D morphological and correlation analysis of grayscale tomograms. Swelling and shrinkage resulted in a complex heterogeneous soil structure which proofed to be very stable when mechanical loads were applied. The mechanism of soil deformation for both structure formation by internal hydraulic stresses and structure degradation by external mechanical stresses were in both cases controlled by pre-existing (micro)-structures. Especially during wetting such structures served as a nucleus for subsequent structure evolution. The results demonstrate the potential of more detailed non-invasive micromechanical analysis of soil deformation processes which could improve the conceptual understanding of the physical behavior of soil systems.