The Queen travelled at the heart of the flotilla of tugs, steamers, pleasure cruisers, dragon boats and kayaks.
The event was the highlight of the Jubilee weekend, but a fly-past has been cancelled because of the weather.
Some 10,000 people joined a Greenwich street party, one of many in the UK marking 60 years of the Queen's reign.
The river event officially started with the ringing of Jubilee bells at 14:40 BST and ended when the last vessel completed the seven-mile route from Albert Bridge to Tower Bridge just after 18:00 BST.
The Queen, dressed in a white hat and a silver and white coat designed by Angela Kelly, was taken to her barge on the launch of the now-decommissioned Royal Yacht Britannia after being greeted by a spontaneous rendition of the national anthem from the crowds.
'Amazing day' She was accompanied by senior royals, including the Duke of Edinburgh and the Duke and Duchess of Cambridge, on the barge, which was decorated with 10,000 flowers from the royal estates.

The Spirit of Chartwell left Cadogan Pier once the rowing boats in the flotilla had safely passed. Leading the rowing boats was the million-pound row barge Gloriana, with Olympic gold medallists Sir Matthew Pinsent and Sir Steve Redgrave among the 18 rowers.
A huge cheer went up whenever the royal barge came into sight of the crowds. Hungarian Laura Konig, 34, who lives in the London borough of Sutton, said: "I really enjoy the music, when the boats with bands come by it's brilliant and the atmosphere is so cool. The weather could be better but apart from that it's an amazing day."
A boat carrying eight specially cast Jubilee bells led the water-borne procession, and churches along the river bank were returning the peal as it passed. There were 10 musical barges, carrying choirs and orchestras.
A collection of small ships used to rescue stranded troops from the beaches of Dunkirk in 1940 also took part, led by the Motor Torpedo boat 102, the flagship of the officer who co-ordinated the evacuation.
The Queen smiled at the sight of a life-size puppet horse - from the play War Horse - which was running along the roof top of the Royal Festival Hall. The Queen pointed out the performance to Camilla.
Dozens of spectators at Tower Bridge were disappointed as security staff blocked off pathways due to fears of overcrowding, more than an hour before the flotilla was due to arrive.
Those who were able to claim a spot on the river were delighted when they could hear the bells shouting "it's happening!" and lifting up little children to see the sight.
Tower Bridge raised as the royal barge approached, with heavy rain returning to the London skies as it moored to allow the Queen to watch the rest of the flotilla pass.
The Guinness World Records said the pageant had set a new world record for the largest parade of boats, surpassing the previous record of 327 in Bremerhaven, Germany, last year.
BBC Big Screens transmitted live coverage of the pageant in 22 locations around the UK including Belfast, Cardiff, Edinburgh, Birmingham, Bristol, Leeds, Liverpool, Manchester and Middlesbrough.
Prime Minister David Cameron paid tribute to the 86-year-old Queen during an interview on BBC One's Andrew Marr programme earlier, saying: "Her insight and her sharpness is extraordinary and I don't see any sign of her working less hard." But his own Jubilee party in Downing Street was moved indoors because of the weather.
In Piccadilly, central London, the BBC's Sangita Myska said there was a "huge crush" as well-wishers flocked to greet a surprise visit by the Duke and Duchess of Cornwall to a street party where 500 tables had been set up.
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