Surface microbiological investigations are critically dependent on the procedures used to collect samples for study. It can be difficult to distinguish between indigenous organisms and those encountered as contaminants during the drilling process. We found that coliform bacteria contaminated drilling mud slurries. These bacteria proved useful as tracer organisms in evaluating the degree of microbial contamination accidentally encountered while drilling for subterranean samples. While these organisms were found in high numbers in both the circulating muds and in the mud reservoir, few subsurface samples harbored conforms. Subsurface slurries did not inhibit the growth of a known coliform inoculum. These results indicate that the methods used to collect and field‐process cores from Atlantic coastal plain sediments were sufficient to prevent a large degree of bacterial contamination in most samples. The microflora in drilling fluids did not quantitatively or qualitatively account for the number and diversity of bacteria in subsurface samples. We conclude that a large and viable bacterial community is present in deep regions of the terrestrial subsurface.