The 39-year-old Briton, who won C2 canoe slalom gold at London 2012, was carried from Waterloo Bridge by four police officers on Sunday evening.
Stott is not among the 40 people who have so far been charged by the Metropolitan Police.
Speaking on Saturday, he said the protests were “really important”.
“I don’t think there is anything more meaningful that I could be doing in my life right now,” said Stott.
“I feel like it is really tough to disrupt people’s lives like this, but this is really important because I believe the disruption that will come down the line if we do not declare a climate emergency and do not tackle this situation of climate change, it will just dwarf any inconvenience here today.”
Stott had shouted of the “ecological crisis” and earlier given a speech while sitting on top of a bus stop.
As of 19:00 BST on Sunday, 963 people had been arrested during the Extinction Rebellion protests in the UK capital.
Thousands of people have been campaigning at sites including Oxford Circus, Waterloo Bridge, Westminster and Marble Arch.