Leaks started to appear in some basements Friday, while some residents on the city's outskirts were forced to travel by boat through waterlogged streets.
The Louvre, Musee d'Orsay and Orangerie museums are on high alert, with the lower level of the Louvre's Islamic arts wing closed to visitors.
A health centre in the northwestern Parisian suburbs, where 86 patients were receiving care, had to be evacuated Friday.
Meanwhile over 650 people were evacuated from their homes in the Paris region, according to police.
The Vigicrues flooding agency scaled back its peak predictions for the river in the capital, saying it will top out at 5.8 to 6 metres (19 to 19.7 feet) between Saturday afternoon and Sunday morning, compared with 6.2 metres previously.
But that would still bring the Seine four to five metres above its normal height, causing headaches for commuters as well as people living near its overflowing banks.
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".
Boat traffic halted
All boat traffic on the Seine in Paris and upstream has been stopped, keeping tourists off the capital's famed sightseeing boats.
But forecasters said the rainfall in recent days had not been enough to push the Seine beyond their expectations.
"We've been reassured, it will keep the water level high but not increase it," said Francois Duquesne of the Vigicrues floods agency, though he warned of the risk for more rain next week.
"If it rains again from the middle of next week, something I'm not sure of at this point, we're not necessarily done with this yet," said Marc Mortureux, risk prevention director at the French environment ministry.
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 outskirts of the capital 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.
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