Soil biophysical transport mechanisms promoting biogeochemical sorption of soluble organic carbon (SOC) compounds within macroaggregates control the retention and release of most soil nutrients, C- and N-based polysaccharides, and contaminants. Ecosystems containing continuous supplies of soluble root exudates and particulate organic matter (POM) provide a constant supply of mobile SOC compounds to surfaces and internal pore networks of soil aggregates. Intra-aggregate pores, especially the ultrafine pores, appear to be developed, interconnected, and blocked or disconnected by repeated drying and wetting (DW) cycling with direct but unknown contributions to movement and retention of SOC compounds. There is evidence that the severity (e.g., range of soil water potential) and frequency of severe DW cycles control intra-aggregate micro- and nanopore formation and function. Heterogeneously distributed microsites within aggregates contain microbial communities that readily mineralize available C and N compounds, producing mobile SOC that can be tightly sorbed to additional mineral surfaces made available within micro- and nanosized fissures during repeated DW cycling. Mechanical removal of concentric soil layers of aggregates, synchrotron imaging and computer microtomographic (CMT) image processing software of three-dimensional pore networks and connectivities, coupled with synchrotron X-ray small angle scattering to measure pore sizes. Natural isotopes of 13C and 15N to quantify C and N sorption and CO2 respiration provide new and integrated approaches for quantifying spatially heterogeneous changes of pore diameters, connectivities, and organo-ion-mineral sorption within intra-aggregate pore networks. Net C and N alterations at surfaces and within aggregates appear to modify both the microbial activities and bacterial community structures, producing integrated feedback and feed-forward processes between the soil biological and physical components of soil aggregates.