The spatial separation of soil organic carbon (SOC), microbes, and extracellular activity is an important mechanism of SOC protection in soils that exists at the soil pore (micron-mm) scale. The microbial processes that control soil C metabolism, and emit greenhouse gases (GHG) to the atmosphere encompass a wide range of chemical compounds, reactions, and products. Potentially labile SOC may be isolated in soil pores, protected from these metabolic processes. We are particularly interested in the role played by hydrology in connecting soil pores and increasing the availability of physically isolated SOC. We hypothesize that the SOC protection mechanisms described in Earth system models (ESMs) are dependent on stable soil conditions, and changing hydrologic connectivity through increased water saturation or disturbance will increase SOC mineralization and GHG fluxes to the atmosphere. We focus our application for EMSL resources on chemical characterization of soil C fractions, physical characterization of pore-scale soil structure, and computational tools to integrate our data for the development of new models of soil C dynamics. The proposed research requests high-resolution chemical and physical characterization to study how soil C is stored in soil macropore networks, and rigorously link soil physical structure, water movement, and C chemistry to elucidate pore-scale mechanisms of soil C protection and metabolism. By coupling new knowledge of the physical and chemical protection of soil organic C with transport simulations, we will develop mechanistic models of soil C dynamics in soil that reflect pore-scale processes and that could therefore increase the predictive power of ecosystem models under changing conditions such as presented by a changing climate.