<p>Urban rivers are essential for human activities and ecosystems. Urban runoff is a major source of various pollutants in urban rivers. In this study, we investigated the effect of rainfall and snowmelt subsequently causing urban runoff in a cold climate region on bacterial community structures and antimicrobial resistance gene concentrations in an urban river in Sapporo city, Japan, which has an average snowfall of 4.8&#xa0;m. Bacterial community structures of the river water were analyzed by next generation sequencing of bacterial 16S rRNA genes. The antimicrobial resistance genes, <i>mphA</i> and <i>bla</i>_IMP, were determined using quantitative polymerase chain reaction. Rainfall and snowmelt increased the effluent discharge rate of treated wastewater, and river water depth. Rainfall and snowmelt also increased <i>Escherichia coli</i> concentrations by 4–20 folds in the river, probably because of combined sewer overflows, urban runoff, or increased effluent discharge rate of treated wastewater to the river. Urban runoff and the subsequent discharge of treated wastewater decreased the bacterial alpha diversity and increased the species evenness of bacteria. Bacterial beta diversity analysis showed that the discharge of treated wastewater caused by rainfall and snowmelt changed the structure and diversity of the bacterial community in the river. The concentrations of the antimicrobial resistance gene <i>mphA</i> were related to the discharge of treated wastewater. In contrast, the antimicrobial resistance gene <i>bla</i>_IMP appeared to be present in the upstream pristine environment. Results of this study should be informative for challenge to reduce the antimicrobial resistance bacteria due to combined sewer overflows by wastewater management authorities.</p>