At least 13 ships could not leave or enter Rotterdam because pilot services - required by large ships or those carrying hazardous materials - were on hold, and strong winds stopped some container terminal operations, a spokesman said.
However, a water defence system which shuts off part of the port, a major transit point for commodities and manufactured goods, had not been activated yet, he said.
Schiphol Amsterdam Airport warned on its website that flight delays and cancellations were expected throughout the day.
The Ministry of Infrastructure warned of high water levels along the coast. Part of the country is below sea level.
Weather conditions are expected to improve later on Thursday, with less rain forecast for Friday, Dutch meteorological institute KNMI said.
KNMI kept its "extreme weather" warning for the three northern provinces but withdrew warnings for the two coastal provinces in the west.
In the northern province of Groningen, near the town of Tolbert, authorities were evacuating about 100 residents from an area where a dyke is at risk of breaking.
The dyke protects about 200 hectares of mostly farm land.
"There is a chance of the dyke breaking - a small chance," said Peter Rehwinkel, chairman of the safety region Groningen.
Some farmers have remained on their land to move animals out of danger, and police sealed off the area, said the municipality of Leek, which includes Tolbert.
Two designated areas will be flooded to limit risks for the cities of Groningen, Hoogezand and Winschoten, the Hunze en Aa's water authority said in a statement.
The southern river city of Dordrecht, about 22 km (14 miles) southeast of Rotterdam, is distributing sandbags in case the river floods lower parts of town, Dordrecht city website said.
A mobile water defence system was set up in and around the northern city of Kampen to protect against the river IJssel flooding, Groot Salland water authority said. (Reuters)
