This research was focused on quantifying the impact of tillage and crop rotation systems on the annual dynamics of soil microstructure. Intact soil cores were collected from long-term management plots at the University of Guelph’s Elora Research Station in Ontario, Canada. X-ray CT scanning was used to obtain high-resolution 3D imagery of each core and specialized plugins were used in ImageJ to segment resolvable voids, then to quantify their abundance and morphology in the binarized imagery. Size, shape and orientation of voids as well as radiodensity and porosity were analyzed. The results between treatments and amongst sampling times were very dynamic. Spring tandem disc and fall moldboard plow tillage systems, and corn-corn-soybeans-winter wheat (red clover) and corn-corn-soybeans-soybeans crop rotation systems showed to be the most dynamic. The management systems not only directly altered soil structure, but also its response to natural factors throughout the sampling seasons.