The application of manure and inorganic fertilizer in row crops may significantly influence soil and greenhouse gas (GHG) emissions. Understanding the long-term influence of these management practices on soil pore characteristics, hydro-physical properties and greenhouse gas emission is essential in developing proper conservation practices. However, there is limited information on the impact of cattle manure and inorganic fertilizer application on soil hydro-physical properties, soil pore characteristics at lower depths and surface GHGs emissions. Therefore, the objectives of this study were to;(i) utilize X-ray computed tomography (XCT) technique to quantify the impact of manure and fertilizer amendments under a corn (Zea mays L.)-soybean (Glycine max L.)-spring wheat (Triticum aestivum) rotation system on soil pore characteristics to the depth of 40 cm;(ii) assess the impact of different manure and inorganic fertilizer application rates on soil profile organic carbon and hydro-physical properties under corn-soybean-spring wheat rotation;(iii) to investigate the impacts of cattle manure and inorganic fertilizer on soil surface greenhouse gases (GHG)[carbon dioxide (CO 2), nitrous oxide (N 2 O), and methane (CH 4)] fluxes from soils managed under corn-soybean-spring wheat rotation. The study was conducted at Brookings (initiated in 2008) and Beresford (2003) in South Dakota. Treatments included: low manure (LM), medium manure (MM), high manure (HM), medium fertilizer (MF), high fertilizer (HF), and control (CK). Four replicated intact cores were collected from all the treatments at 0-10, 10-20, 20-30, and 30-40 cm depths.