The structural and functional properties of the bacterioplankton in two small rivers and the Sheksna River that run through the large industrial city of Cherepovets were studied from April to October 2009–2011. The three-year average numbers and biomass of planktonic bacteria in small rivers were 18.7–18.8 million cells/mL and 3.5–4.9 g/m 3 , respectively; these values in the Sheksna River’s littoral zone were 15.8 million cells/mL and 2.2 g/m 3 . The bacterioplankton production in the small water courses exceeded that in the Sheksna River by a factor of 1.8–2.2. The contribution of bacterial filaments to the total biomass and the total bacterioplankton production increases in small polluted rivers.