The pageant evoked a time when it was vital to London, and to Britain. Monarchs used the river as their main highway for centuries, and river processions were once common in London. The last comparable royal pageant was held for King Charles II in 1662, when diarist Samuel Pepys recorded boats so numerous he could "see no water."
At Tower Bridge - the final bridge before the river reaches the sea - a fanfare rang out and the two blue arms known as bascules were raised in salute to the royal boat.
The pageant was a visual spectacle, accompanied by a wall of sound. The river rang with spectators' cheers, ships' horns, church bells and the sound of barge-borne bands playing everything from Handel's "Water Music" to Bollywood anthems and - as the vessels passed the headquarters of the MI6 spy agency - the James Bond theme.
The pageant ended with a slightly soggy burst of fireworks over Tower Bridge - and news from Guinness World Records that it had broken the record for largest parade of boats.
The four-day Diamond Jubilee celebrations also included thousands of street parties across the country on Sunday. Prince Charles and his wife Camilla, Duchess of Cornwall, joined hundreds of people for a damp al fresco lunch on Piccadilly, one of London's main shopping streets.
But a lunch organized by Prime Minister David Cameron's staff in Downing St. was moved indoors because of the rain.
Not everyone in Britain was celebrating. Hundreds anti-monarchists held a riverbank protest to oppose the wave of jubilee-mania - though their chants were quickly countered by renditions of "God Save the Queen" from pageant-goers.
"People are sick and tired of being told they must celebrate 60 years of one very privileged, very remote and very uninspiring head of state," said Graham Smith of the anti-monarchist group Republic. "The hereditary system is offensive to all the democratic values this country has fought for in the past."
Jubilee celebrations kicked off Saturday with a royal day at the races, as the queen - a racing fan and horse breeder - watched a horse with the courtly name of Camelot win the Epsom Derby.
The events end Tuesday with a religious service at St. Paul's Cathedral, a carriage procession through the streets of London and the queen's appearance with her children, grandchildren and great-grandchildren on the palace balcony.
The queen took the throne in 1952 on the death of her father, King George VI, and most Britons have known no other monarch.
Many who stood in the rain for hours along the river Sunday for glimpse of their monarch said it had been worth it.
"It really was exciting, it's one of those moments, said 41-year-old Sarah O'Connor. "She's on our stamps, our coins, our post boxes - she is our queen. God save the queen."