The physicochemical properties and bacterial community in sediments of Lake Shiraishi, a lake with brackish water, were characterized to elucidate the influence of oyster farming and seawater and freshwater inflow. Physicochemical analyses suggested the marine origin of the sediment at the mouth of the lake, while higher organic matter load and the resultant anaerobic, reductive condition of the sediments of the inner part were observed. The bacterial community in the sediments reflects these sediment environments: the bacterial community in the vicinities of oyster farms included sulfate-reducing bacteria (SRB) , although sulfur-oxidizing bacteria (SOB) were found at all the sampling sites. In addition, similarity of the band profiles obtained with 16S ribosomal RNA gene (16S rDNA) -denaturing gradient gel electrophoresis (DGGE) decreased in proportion to the distance from the mouth of the lake to the oyster farms in the inner part. This study was able to characterize the microbial community shift in brackish lake sediments with an oyster aquaculture system through the molecular fingerprinting technique, DGGE, in relation to their physicochemical characteristics.