Amsterdam’s Schiphol Airport, one of Europe’s busiest airports, suspended all air traffic on Thursday as gusts of up to 85 mph blew in along the coast.
At least 260 flights were scrapped and falling roof tiles led to the closure of airport terminals.
Nationwide train services and many tram and bus services were halted after the highest weather alert was issued.
Police said three people were killed by falling trees or debris in separate incidents.
In Rotterdam, shipping containers were toppled and entire roofs ripped off homes, local TV showed.
Schiphol later said some flights would resume as the storm moved inland, but that there would be severe delays.
Two departure halls remain closed.
Dutch Twitter users took to social media to post pictures of trucks and trees blown over by the ferocious winds with the hashtag #coderood.
In Germany, railway operator Deutsche Bahn said it had suspended all services in the western state of North Rhine-Westphalia, the country’s most populous, leaving hundreds of thousands of travellers and commuters stranded.
Deutsche Bahn said:”Since this affects many long-distance connections, there are effects on the entire rail services, also internationally.”
In Munich, eight domestic flights by Lufthansa were cancelled, the airport operator said