Accumulations of more labile Carbon (C) and Nitrogen (N) biopolymers in exterior regions of macroaggregates promote microbial activities and increase hydrophobic properties at aggregate surfaces. Numerous soil aggregation processes including drying-wetting cycles constantly alter the spatial gradients of ions and soluble compounds within macro-aggregates. Drying-wetting cycles accumulate greater concentrations of C and N at the surfaces of macro-aggregates and promote the inward flux of these compounds for prolonged storage. Consequently water repellency, predominately located at aggregate surfaces can be increased within aggregates, depending on the amounts and the chemical properties of Soluble Organic C (SOC) generated by different types of crop residues. C concentrations in macro-aggregates of No illed (NT) were 220% greater than moldboard plowed Conventionally Tilled (CT) for glacially deposited silt loam soils and 160% greater for silty clay loam soils. Greater C concentrations were observed in the exterior layers of CT aggregates from these soils but not for NT aggregates with greater intra-aggregate porosities. Increased numbers of bacteria were observed in the exterior regions of macro-aggregates. Concentrations of microorganisms (fungi and bacteria) were also greater in exterior regions of aggregates from luvisols derived from loess. Carbon contents of macro-aggregates are positively correlated with bacteria populations, aggregate stability, and intra-aggregate porosities. Our results indicate that natural drying-wetting cycles enhance the internal migration of C into macro-aggregates and increase the stabilization of intra-aggregate pore networks, promoting the flux of SOC deeper into interiors of macro-aggregates. Stable micro-pore networks increase the retention of carbon with feed-back mechanisms that promote aggregate stability. Greater knowledge of these unexplored process-level mechanisms will lead to improved soil management practices that enhance the sequestration of C by soils.