A total of 472 samples of soft-shell clams ( Mya arenaria ), collected from three major clam harvest areas in the Chesapeake Bay and dockside check stations, was analyzed for standard plate count (SPC), total coliforms, fecal coliforms, Escherichia coli , and coliphages. SPC increased during the summer season. SPC geometric means of 2.6 × 104, 6.9 × 104, and 7.2 × 104/g, respectively, were found in three major harvest areas. Fecal coliforms remained relatively stable with geometric means of 30, 54, and 62/100 g. As seasonal temperatures increased, the total coliform geometric means declined slightly ranging from 1,500 to 6,300/100 g. E. coli means were low (< 27/100 g). The occurrence and levels of male-specific coliphages were also low and did not correlate with bacteriological quality. No significant microbiological quality difference was found between soft-shell clams sampled from harvest waters and check stations. Results indicate that the microbiological quality of soft-shell clams either at harvest or check stations was satisfactory.