Activists blocked a section of a motorway during the afternoon in protest against Dutch fossil fuel subsidies.
Police said they had used water cannon to disperse activists blocking a major road in the city, and arrested "a total of 1,579 people... 40 of whom will be prosecuted" on charges including vandalism.
One of the activists bit a policeman during his arrest, police said.
According to Extinction Rebellion, some 7,000 people gathered to join the demonstration.
Anticipating the water cannon, some wore swimsuits or carried umbrellas as they sat in protest across the A12 motorway, holding banners and signs.
The protest marks the seventh organised by Extinction Rebellion in the same section of motorway at The Hague, close to the parliament and main ministry buildings.
But Saturday saw the highest number of people arrested at a protest yet, according to Dutch news agency ANP.
"We're going to stay here until they drag us away," said postgraduate student Anne Kerevers, 31.
"Climate change is an unfolding crisis and we know the cause and it's still being subsidised by our government and it needs to stop," she told AFP.
Several Dutch celebrities were among the protesters, including actor Carice van Houten, best known for her role as Melisandre in the hit TV series "Game of Thrones".
Van Houten posted a video on Instagram showing herself wearing a red poncho, getting drenched from a water cannon.
ANP reported that she was arrested and later allowed to return home, but did not specify whether she was among those who will be prosecuted.
'Broad support'
Police said they had repeatedly "given activists the opportunity to end their action and leave" before using the water cannon and making arrests.
"We've been coming back every month, or every two months, and every time the number (of protesters) has doubled," said Aaron Pereira, a spokesman for Extinction Rebellion.
"There is broad popular support for real climate action and people are waking up to the fact that the government is actively going against this by subsidising the fossil fuel industry."
The environmental campaign group, shortened to XR, has become known for the disruptive and headline-catching stunts which have become their trademark.
In recent years the group has caused huge disruption, hitting roads, airports and other public transport networks with direct action protests against climate change.
But in January it called a temporary halt to its high-profile stunts, and instead promised to mobilise huge numbers against what it sees as government inaction against global warming.
In April it held four days of action in London, including mobilising thousands to rally outside the UK parliament.
In recent months it has also rallied at airports across Europe, including protests at Eindhoven airport in The Netherlands in March.
This week it joined other groups in demonstrating against Europe's biggest private jet sales fair in Geneva.
Some activists chained themselves to the planes on display, and air traffic was briefly disrupted at the airport due to people on the tarmac.
