World leaders had left Hamburg after the G20 summit, but tension on the streets boiled over, with more violence into the early hours of Sunday morning.
Clashes have marred the gathering of the Group of 20 leading economies yet Saturday had seen good-natured protests until things turned ugly late on.
And when bottles and other objects started to be thrown, police turned on the water cannon.
Emergency services said they were treating injured people but gave no numbers.
Chancellor Angela Merkel has faced criticism for hosting the summit in a big city despite the risk of violent protests against capitalism and globalisation.
Over recent days, more than 200 police officers have been injured in clashes and over 140 people arrested.
Hamburg residents are also angry at the damage caused. Merkel says they will receive compensation.
Merkel, who met police and security forces after the summit to thank them, condemned the violence but stressed that the majority were peaceful and legitimate protesters.
The head of Hamburg police earlier expressed shock at the “wave of destructive anger”, rioting and arson since Thursday.