Heavy flooding closed locks at both ends of Germany's Kiel Canal, while the port of Hamburg stopped all vessel traffic.
The Thames Barrier in London was closed and the flood barrier was lowered at the port of Hull on the UK east coast.
The surge barrier in Rotterdam was initially kept open however.
The BBC said the storm surge at Hull reached 5.9 metres, the biggest on record. Thousands of homes were evacuated in the UK.
Hamburg saw its biggest floods for 37 years as water levels rose 4 metres, Bloomberg reported.
No casualties were reported.
Ferry services to the Isle of Man from the UK were suspended.
