The cruise ship, carrying 217 of the 392 German athletes who competed at the London games, was accompanied by around 60 smaller boats as it sailed into the northern city's harbour.
The dapd news agency reports that up to 5,000 supporters were on hand to greet their heroes after a 36-hour journey from London.
Miriam Welte, gold medal winner in the women's cycling team sprint with Kristina Vogel, said "we knew a few people would be waiting for us, but we didn't expect so many."
Germany won 44 medals in London, including 11 golds.
The athletes were to be honoured later by Hamburg's mayor Olaf Scholz among others.