AbstractFish abundance and size composition in a 28 km stretch of the Vltava River in the Czech capital of Prague were studied using horizontal dual‐beam scientific sonar. Very low fish densities (0.6–0.7 fish/100m3) were found above Prague where the river is influenced by a cascade of reservoirs. These have a retention time of more than 100 days and release hypolimnetic water. A significant increase in fish density was found in the Berounka River confluence (a tributary with a normal, seasonal temperature pattern) just above the city (about 10 fish/100 m3). The fish stock is fairly low in the city itself because of channelization of the river bed (1.3–3.5 fish/100 m3), but much greater densities (14.9–16.9 fish/100 m3) were found below the city where the river receives a high organic load of partially treated sewage and has a semi‐natural shoreline. The largest average fish size and biomass were also reported from this section.