Soil biophysical and biogeochemical mechanisms of solution transport within macro-aggregates control the retention and gauged release of most soil nutrients and influence the stability of soil aggregates. Soil drying and rewetting (DW) provide additional carbon (C) and nitrogen (N) substrates for microbes and increases mineral surfaces among intra-aggregate porosities. Soil carbon contents in aggregates from no tillage (NT) systems, subjected to fewer and less severe D/W cycles contained 1.6 and 2.2 fold greater C contents than conventional tillage (CT) systems. C and N compounds from plant roots contributed up to 66% of the C and increased N within exterior regions of field aggregates. The net diffusion of root C compounds into aggregates approached 7 x10-4 mm h-1 during 20 months of field conditions. Synchrotron imaging and computer microtomographic software provide new approaches for quantifying spatial distributions of intra-aggregate pore sizes and connectivities within aggregates. Rhizosphere aggregates are more stable, which leads to greater C sequestration. HYDRUS-2D models were used to predict texture and porosity controls of solution transport through the exterior regions of aggregates, reflecting heterogeneous dehydration patterns which could modify resorption of soluble C and other substrates. These C and N alterations within aggregates influence biophysical feed-back and feed-forward processes that directly control both soil C sequestration and aggregate stability.