In 2015, the bacterioplankton of the Neglinka River, a tributary to Lake Onegо draining the territory of Petrozavodsk, was studied. Ten storm drains empty into the river without treatment, making up a third of the river’s total streamflow. As the river flows through the urban area, the number of ecological and trophic groups of bacterioplankton and pathogenic microorganisms in the water increases. The quantitative indicators of bacterioplankton featured significant differences between the suburban and urban parts of the river. The seasonal patterns of the studied bacterioplankton indicators are shown to have little correlation with the hydrological and temperature regime of the river, reflecting the influence of polluted runoff from the urban area. The high number of indicator groups of bacterioplankton (heterotrophic, saprophytic, phenol-oxidizing and hydrocarbon-oxidizing bacteria, total coliform bacteria) points to severe pollution of the river water with various organic substances, including those of fecal origin, as well as petroleum hydrocarbons and phenolic compounds.