We investigated the horizontal distribution patterns of bacterial community compositions (BCC) and extracellular enzyme activities (EEAs) from the mouth of Yasu River to the pelagic region of Lake Biwa at six stations along a 9.6-km horizontal transect. Surface water samples were collected along the set transect from November 2012 to September 2013. The concentrations of dissolved nitrogen and phosphorus in the near-shore region were higher than those in the lake. Betaproteobacteria and Bacteroidetes dominated in the river mouth, whereas Alphaproteobacteria and Actinobacteria dominated in the lake. β-glucosidase and cellobiohydrolase activities in the near-shore region were higher than those those in the lake, and the alkaline phosphatase activity did not differ from the river mouth to the pelagic region. In contrast to a clear difference in BCC and EEAs between river mouth and lake, the differences in BCCs and EEAs among stations in the lake were insignificant. The less heterogeneity of BCC and EEAs in the lake indicated that the effects of river to the BCC and EEAs in the surface layer of lake is limited to the near-shore region.