Police reportedly dragged away at least three campaigners who doused the fountain at the end of The Mall in paint and dyed the water a dark crimson on Thursday.
Protesters let off flares as they stood in the fountain holding up placards which read: “A royal blood bath.”
By Wednesday nearly 200 people had been arrested at XR demonstrations in London during the first four days of disobedience by the climate action group.
At least 10,000 people have taken part in the rallies, which started on Sunday and are due to run for two weeks.
The Brazilian embassy, Piccadilly Circus, HMRC and the Department for International Trade (DIT) have also all been targeted.
The group gave the DIT a mock award for "making an outstandingly awful contribution to climate change".