The primary transport of pathogenic microorganisms in soils occurs through macropores that bypass the filtering and adsorptive effects of the soil. Recent research indicates immediate breakthrough of solutes and contaminants in subsurface drainage by extraordinarily efficient transport through directly connected macropores. In this study, an innovative soil column packed with loamy sand soil was used to simulate the transport of E. coli through directly connected macropore into the subsurface drainage systems. Four experiments simulating open surface connected and buried macropores were performed. The soil column was flushed with distilled water, diluted swine manure, and finally with distilled water at 0, 48, and 96 hours, respectively, after packing. Both open surface connected and buried macropores were capable of transporting E. coli to the subsurface drain. During the manure flushing, breakthrough time in both discharge and E. coli was inversely proportional to the macropore length. In the macropore, E. coli detection occurred simultaneously with macropore discharge breakthrough. For open surface connected macropores that extended the entire distance between the soil surface and drain except for the last 10 to 20 cm, the maximum E. coli concentrations in the drain flow was approximately 20 to 30% of the inflow E. coli concentration. For buried macropores, maximum E. coli concentrations in the drain flow were approximately 10% of the initial concentration but 25 to 40% in the macropore. The highest E. coli recovery concentrations occurred during the final distilled water flush, approximately 48 hours after manure application. It was hypothesized that these peak concentrations were due to the development of an E. coli pool within the capillary fringe. The findings of this study stress the importance of directly connected macropores to subsurface drainage systems in allowing E. coli to bypass the soil filter capacity, especially after rainfall events or irrigation following manure application.