Protection of water systems from non-point source pollution remains an important environmental challenge. Particularly in rural and now mixed use watersheds, runoff often carries nutrients, pesticides and pathogenic microorganisms which impair waters that fail to meet water quality standards associated with designated uses. E. coli, as an indicator of microbial water quality and public health risk, is used throughout the world for surface and ground water studies. Yet, in rural agricultural settings, the fate of E. coli after application of animal manure or deposition of animal waste to soils is not well understood. It is clear that filtration, adsorption and die-off are processes in the soil which impact the transport of these bacteria, however, differential survival, desorption and regrowth are likely occurring as well and are dependent on soil micro environments. We are combining synchrotron x-ray microtomography identification of intra-aggregate pore geometries with saturation kinetics of E. coli, cations, anions, and C moieties from single aggregates encased in glass beads of different diameters. These noninvasive methods have been used to identify unique sorption/desorption patterns of ions and bacteria coupled with soil respiration rates generated by stable and unstable soil aggregates subjected to multiple pore volumes of simulated soil solutions. These patterns of biogeochemical interactions appear to be further modified by rates of solution absorption by soil aggregates as flux rates are modified by the average diameters of pores, expressed by different sized glass beads adjacent to aggregate surfaces.