This paper presents an agricultural residue removal decision framework that couples the environmental process models WEPS, RUSLE2, SCI, and DAYCENT. One of the goals of this integrated model is to quantify the impacts of land management strategies on soil organic carbon and CO2 emissions. Soil, climate, and land management practices are considered in determining sustainable residue removal rates using wind- and water-induced soil erosion and qualitative soil organic carbon constraints and to quantify the long-term impacts of sustainable residue removal on soil organic carbon and greenhouse gas emissions. Using this integrated model sustainable residue removal for four crop rotations, three tillage regimes, and four soil types representing nearly 70% of the arable acres in Boone County, Iowa are examined. Each scenario was performed for a twenty-year period. Soil organic carbon and CO2 emission results are aggregated by soil type using crop rotation and tillage statistics. The soil type results are aggregated using a normalized percentage area to provide a county level estimate of soil organic carbon changes and CO2 emissions. Results show that for the largest sustainable residue removal rate that soil organic carbon increased 3.53–6.63 Mg/ha over the 20 year simulation and that CO2 emissions ranged from 3.50–4.23 Mg/ha across the four soil types resulting in an average increase of soil organic carbon of 4.85 Mg/ha and CO2 emission of 3.77 Mg/ha at the county level.