The U.S. agricultural sector is in a prime position to provide crop residues, including corn stover, as a feedstock for large-scale biofuel production. However, stover protects soil from the forces of wind and rain, and when removed can accelerate soil erosion and lead to reductions in agricultural sustainability and environmental quality. Previous research has indicated that the impacts of stover removal are site and soil-specific. Therefore, stover harvest rates that limit the negative impacts on agriculture and the environment must be established on a regional basis. We assessed the effects of variable levels of corn stover removal on soil properties on a regional scale across three contrasting locations (Colby, Hugoton, and Ottawa) in Kansas. Five stover treatments that consisted of removing 0, 25, 50, 75, and 100% of corn stover after harvest were studied for changes in bulk density (ρb), water stable aggregates (WSA), soil organic C (SOC), soil water content, soil temperature, and water retention over time. Soil bulk density and water stable aggregates (WSA) were measured periodically, while soil water content and temperature were collected continuously throughout the experiment using automated sensors. Results of this regional study showed that soil bulk density was highly variable and apparently unaffected by stover removal at all locations. Aggregate stability and soil water content decreased with increases in stover removal rate at all sites. Soil temperature tended to fluctuate much more heavily in plots with high amounts of stover removal, compared to low removal rates. Soils with low stover removal rates were able to retain more water than soils with high removal rates. Our results from the first two years of stover management suggest that high rates of stover removal for cellulosic ethanol production can affect soil physical properties in ways that are detrimental to agricultural sustainability.