From a peak of 6.10 meters (20 feet) in the early hours of Saturday, the river began to subside, falling to 5.77 meters at 8 a.m., the environment ministry's Vigicrues flood watch website said.
However, red alerts had been issued for the Seine-Maritime and Eure departments in the northern Normandy region but were lifted early Sunday and they passed on to the next level of orange.
Alerts have also been issued in 15 other regions, including Ile-de-France, where Paris is located, Lorraine in the northeast as well as parts of the country's central areas. Meteo France has forecast showers on Sunday across much of the country.
The authorities in Seine-Maritime said there had "been no significant damage so far."
Traffic has been prohibited in some areas of Normandy and although the Seine had risen in the northern city of Rouen, it did not break its banks.
"It's like this when there are strong tides," said a port official, AFP reported.
Across Europe, at least 18 people have been killed in floods that trapped people in their homes, felled trees and power lines, cut off roads and rail lines and forced rescuers to navigate swamped streets in lifeboats.
In Paris, the Louvre and Orsay museums, which sit on opposite banks of the Seine, were closed for a third day Sunday, after shutting their doors in a race to move art treasures out of basements to higher ground as a precautionary measure.
They are only due to reopen Tuesday.