The spatial distribution of bacterioplankton communities in rivers is driven by multiple environmental factors, including local and regional factors. Local environmental condition is associated with effect of river water chemistry (through species sorting); ecological process in region is associated with effects of land use and geography. Here, we investigated variation in bacterioplankton communities (free-living, between 0.22 and 5 μm) in an anthropogenically disturbed river using high-throughput DNA sequencing of community 16S rRNA genes in order to investigate the importance of water chemistry, land use patterns, and geographic distance. Among environmental factors, sulfate (SO42–), manganese (Mn), and iron (Fe) concentrations were the water chemistry parameters that best explained bacterioplankton community variation. In addition, forest and freshwater areas were the land use patterns that best explained bacterioplankton community variation. Furthermore, cumulative dendritic distance was the geographic distance parameter that best explained bacterial community variation. Variation partitioning analysis revealed that water chemistry, land use patterns, and geographic distances strongly shaped bacterioplankton communities. In particular, the direct influence of land use was prominent, which alone contributed to the highest proportion of variation (26.2% in wet season communities and 36.5% in dry season communities). These results suggest that the mechanisms of species sorting and mass effects together control bacterioplankton communities, although mass effects exhibited higher contributions to community variation than species sorting. Given the importance of allochthonous bacteria input from various land use activities (i.e., mass effects), these results provide new insights into the environmental factors and determinant mechanisms that shape riverine ecosystem communities.