Howling winds of up to 146 kmh (90 mph) battered the country as Storm Poly crashed into the North Sea coast, downing trees and prompting Dutch authorities to warn people to stay at home.
Amsterdam's Schiphol Airport said a combination of strong winds, rain and poor visibility meant there would be "very limited air traffic" for both incoming and departing flights until at least 3pm (1300 GMT).
More than 300 flights were cancelled at Schiphol, a major hub for connecting flights from Asia, the Middle East and the United States to the rest of Europe, public broadcaster NOS said.
Trains were halted in the north of the country for safety reasons while a key motorway at Alkmaar, near Amsterdam, was blocked by a toppled lorry, Dutch authorities said.
The Dutch meteorological service KNMI issued its highest "code red" warning for four northern regions, meaning severe disruption was possible.
The government sent out a mobile phone alert calling on people to stay indoors in North Holland province, which includes Amsterdam, and to only call overstretched emergency services in "life-threatening" situations.
Winds of force 11, the second highest on the scale, were measured in the northern port of IJmuiden making it the "first very severe summer storm ever measured" in the country, Dutch weather service Weerplaza said.
A gust of 146 kmh measured in IJmuiden was also the strongest ever recorded in the summer in the Netherlands, where the storm season is normally from October to April, it said.
With around a third of the country lying below sea level, the Netherlands is particularly vulnerable to extreme weather and the effects of climate change, and has a huge system of dykes and other water defences.
A violent North Sea storm on the night of January 31 to February 1, 1953, killed more than 1,836 Dutch people.
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