This research investigates soil nitrogen and carbon after 12 years of vegetable production. The agricultural treatments investigated were a factorially-designed study with a whole-plot tillage treatment (conventional tillage vs. strip-tillage), a whole-plot input treatment (conventional chemical fertilizers and pesticides vs. organic fertilizers and pest control) and a split-plot rotational crop treatment (3-year vegetable rotation vs. continuous stake tomatoes). The field site was located in the Appalachian Mountains of North Carolina at the Mountain Horticultural Crops Research Station on a fine-sandy loam soil. We examined soil total carbon and nitrogen, and available ammonium and nitrate by depth midsummer of the twelve year of this long-term rotation to determine how much these systems would change in the distribution of the above chemical properties. We determined that the most important treatment factors affecting the soil distribution of nitrogen and carbon in agricultural ecosystems were, in order of importance, tillage, input, and rotation.