The queen, 86, rode a royal barge at the head of the 1,000-ship flotilla for seven miles while hundreds of thousands watched.
But some other pageant events did not survive the soggy weather, the BBC reported. The cannons set to shoot confetti and a helicopter fly-by were canceled.
Some pageant-goers were prevented from reaching the city by overcrowded trains, the report said, while others stayed at home to celebrate. Nearly 9,500 roads were shut across England and Wales for parties, the BBC said.
Worldwide celebrations were under way Sunday throughout the Commonwealth for the queen's Diamond Jubilee of 60 years of rule.
Much of Britain had wet weather, ranging from drizzle to steady rain, but celebrations went on regardless, The Daily Telegraph said.
The newspaper said in England and Wales, there had been almost 10,000 applications for road closures to allow for parties. Belfast in Northern Ireland was hosting a formal tea party at city hall, while Edinburgh, Scotland, had 10 street parties under way.
Celebrations were held elsewhere in the Commonwealth, including Australia, Bermuda, Canada, Jamaica, New Zealand and many of the 42 other countries.
Meanwhile, anti-monarchists said they would stage a protest in London at the Tower Bridge, where the flotilla would disband Sunday afternoon, the Telegraph said.
Among the placards and banners they were carrying were some saying ''citizen not subject'' and ''democracy not monarchy.''