Option 1: The Seine is a river in France and does not flow in Germany, so it is not the correct answer.

Option 2: The Volga is the longest river in Europe and flows mainly in Russia, so it does not flow in Germany. Therefore, it is not the correct answer.

Option 3: The Danube is a river that flows through several European countries, including Germany. It is the second longest river in Europe and is indeed a river that flows in Germany. Hence, this is the correct answer.

Option 4: The Thames is a river in England and does not flow in Germany. Hence, it is not the correct answer.

Therefore, the correct answer is option 3, the Danube.