SNCF explained that with water levels expected to hit 5.75 metres later tonight authorities were forced to take action to prevent the flooding of the tracks between Saint Michel and Musée d’Orsay.
They have shut down four cooling vents located between the tracks and the river to avoid them being flooded, which has forced them to close the line.
Passengers are invited to take Metro Lines 10 and 6 as alternative travel.
RER C will continue to operate on the rest of the line, outside Paris.
But while the situation was improving in other parts of the country, it was worsening ion Paris.
Parts of the right bank of the Seine were closed to vehicles and river traffic was halted out of precaution.
Restaurants and bars along the Seine were particularly badly hit by the flood waters.
The owner of the Baody restaurant, near Austerlitz station, that was partly submerged told The Local: "This is terrible for us. I have no idea when we will be able to reopen.
"Yesterday we put the furniture on the tables, but today we will have to move it all to the river bank. It's a disaster for the business."
Men remove furniture from the Boady restaurant, the owner tells us this is "terrible" for his business pic.twitter.com/lyv7p5c1BN— The Local France (@TheLocalFrance) June 2, 2016
Further down the river the owners of the restaurant La Barge du Crous de Paris, were equally dismayed.
"Luckily the restaurant is raised but we could lose lots of clients this week if the flooding doesn't recede. Just as the tourist season starts too," the owner told The Local.
A policewoman directing traffic by the banks of the Seine nearby described the choas.
"There is terrible traffic because of the floods. Roads are closed. It's been like this for the past couple of days and the flooding just seems to be getting worse," she told The Local.
An elderly Parisian man walking by the Seine told The Local on Thursday: "We have lived here for years and this is not the first time I have seen the Seine flood but it's definitely one of the most exceptional cases. We hope the waters stop rising."
A crisis cell has been set up in the capital to keep an eye on the river and to prepare for any action if necessary.
Experts say Paris is still a long way from facing the catastrophe of the “flood of the century” – a repeat of the 1910 great flood.