Additional police were deployed to monitor the gathering along the Utrechtsebaan Highway at the Bezuidenhoutseweg-Prins Clauslaan intersection near the Central Station.
More than 1,500 climate activists from the climate change protest group, the Extinction Rebellion were arrested on Saturday for blocking a major highway in The Hague.
The police reportedly managed to remove the protesters from the A12 in the late afternoon, who had gathered to denounce the impact of fossil fuel subsidies on the economy and environment.
Verified video footage captured at the event showed the police used water cannons on the protesters for several hours and later managed to clear the road using police vans.
Some 850 demonstrators have already been released without charge. While some sustained minor injuries, the protest remained mostly peaceful.
Around 3,000 protesters took part in the march, which began at noon local time in scenes echoing a similar protest last month.
During the most recent blockade in March, some 700 activists were arrested.
Dutch authorities had refused the demonstrators permission to block the highway on Saturday, and police said they deployed a water cannon after the protesters failed to heed an order to disperse.