The Weihe River is the largest tributary of the typically sediment-laden Yellow River in China. Assuming that high sediment concentrations may increase the turbidity of water bodies, and therefore affect riverine ecosystem, in which the bacterioplankton are crucial components and serve as important indicators of environmental and ecological status through their structure and response to the environment change, it is essential to deep understanding the bacterioplankton structure and influencing factors in turbid and clear river ecosystems. Here, high-throughput sequencing was used to analyze the differences in bacterioplankton structure and major determinants in the typically turbid Weihe River and its clear tributaries from the northern foot of the Qinling Mountains from October to November 2017 and April to May 2018. The results demonstrated that bacterioplankton communities shared similar dominant subcommunities in the Weihe River mainstem and its tributaries, mainly consisting of Proteobacteria and Bacteroidetes phyla and Flavobacterium and Acinetobacter genera. The Faith phylogenetic diversity (PD) index was significantly higher in the turbid mainstem than in the tributaries and was related to turbidity (Turb). Variation partitioning analysis (VPA) showed that geographical distance exhibited notable influences on the community composition in the mainstem; however, the communities in the tributaries had a much stronger response to local environmental factors. Bacteria exhibited a significant distance-decay relationship in the mainstem, whereas geographical distance was not correlated with community dissimilarities in the tributaries. Chlorophyll a emerged as the major determinant of the bacterioplankton structure in the turbid Weihe River, indicating the importance of phytoplankton-bacterioplankton relationships in the turbid river system. These results provide important insights into future research on microbial ecology, environmental monitoring and classified management in diverse river systems.