The river reached 5.7 metres at 9:00 am on Saturday, more than four metres above its normal height, causing headaches for commuters as well as people living near its overflowing banks.
Forecasters believe it will continue to rise, peaking on Sunday night or Monday, but will not reach the 2016 high of 6.1 metres, when the Louvre museum was forced to close its doors for four days.
But the world's most visited museum was on high alert on Saturday, along with the Musee d'Orsay and Orangerie galleries, with the lower level of the Louvre's Islamic arts wing closed to visitors.
Leaks had started to appear in some basements on Friday, while some residents on the city's outskirts were forced to travel by boat through waterlogged streets.
A health centre in Paris's northwestern suburbs, where 86 patients were receiving care, was also evacuated on Friday.
In total more than 650 people have been evacuated from their homes in the Paris region, according to police, while more than 1,400 were without electricity.
The Vigicrues flooding agency scaled back its peak predictions for the river in the capital, saying it will top out at 5.9 to 6 metres on Sunday evening at the earliest, compared with 6.2 metres previously.
"Due to the spread of flooding to different tributaries, the level of the Seine in Paris will continue rising again on the weekend," said Vigicrues, adding that highest level would last for about 10 hours before slowly going down.
It's enough to worry Joao de Macedo, janitor at a residential building in Paris's upscale 16th Arrondissement.
"There are six studios in the basement, and we've had to set up blocks outside to keep the windows from breaking and covering everything in water," he said.
Inside the studios, tables and dressers have been lifted off the floor as water seeps through the walls.
Outside, where the river was nearly lapping the tyres of parked vehicles, a young woman said it was "great to see ducks instead of cars".
The December-January period is now the third-wettest on record since data collection began in 1900, according to France's meteorological service.
All boat traffic on the Seine in Paris and upstream has been stopped, keeping tourists off the capital's famed sightseeing boats.
But flooding like that of 1910, which saw the Seine rise to 8.62 metres, shutting down much of Paris's basic infrastructure, looks unlikely.
More favourable weather is expected for the week ahead, and Vigicrues has lowered its warning level from orange to yellow in several areas upstream of the capital.
But even once the water levels start to recede, forecasters say it will be a slow process, since much of the ground in northern France is already waterlogged.
A main commuter line, the RER C, has halted service at Paris stops through Wednesday, and some expressways that run alongside the Seine have been closed.
In Paris the Seine flows through a deep channel, limiting the potential flooding damage to riverside structures.
But several areas on the city's outskirts are under water, such as the southern suburb of Villeneuve-Saint-Georges, where some residents were getting around by boat and dozens have been evacuated from their homes.
In the south of France, heavy rains caused a breach in the water supply pipe of a holding tank on an oil platform in La Mede, near Marseille, on Saturday, French giant Total said.
Contaminated water, not concentrated crude oil, had leaked, Total said in a statement.