Past research had demonstrated the ability of E. coli to regrow in the soil environment, to survive and finally to be released during saturated conditions. Knowledge of the exact pore locations within soil aggregates opens new opportunities for understanding soil microorganism movement and functioning. The objectives of this study are 1) to determine the feasibility of qPCR technique in recovering E.coli in soil environment; 2) to identify areas within soil aggregates from different managements accessible to E. coli and 3) to study the redistribution pattern of E.coli within soil aggregates and relate E. coli movement within aggregates to the aggregates’ internal pore structures and pore distributions in the aggregates of the three studied soil treatments, namely, onventionally tilled (CT) and no-till (NT) corn/soybean/wheat rotation and native succession vegetation (NS) on Typic Hapludalfs of the Kalamazoo (fine-loamy) series at NSF Long-Term Ecological Research site, southwest Michigan. The results showed qPCR techinique was reasonable for detecting E.coli cells in soil media. CT aggregates displayed significantly greater porosity than NS and NT aggregates. It was also showed that CT contains larger number of medium sized pores (45-90 microns) than the other two treatments. Most of the seeding E.coli cells were remained within the aggregates (~99%) under the saturated condition even when water was evacuated, however, they were found to be greatly redistributed within the soil aggregates. Despite large variability, E.coli spatial distribution was somehow related to pore tortuoisities and connectivities.