Hello how may I help you? I was wondering which river goes through Prague? The Danube river goes through Prague. Are there any other rivers that go through Prague? The Vltava river goes through Prague. Can you tell me another river that goes through Prague? The Elbe also goes through the Czech republic. Which of the rivers that go through Prague is the largest The Vltava river is the most notable river that goes through Prague. Do the Elbe and Vltava rivers intersect at all? They do not.