The library, which includes material from the suffragette movement and letters from Virginia Woolf, Florence Nightingale, Queen Victoria and Sylvia Pankhurst, is housed in a basement at London Guildhall University.
On Wednesday night and Thursday heavy rains in London overloaded the capital's drainage system and several inches of water seeped into the room through the floor.
Once flooding was discovered early on Thursday, staff were summoned from home to move priceless items into secure storage elsewhere in the university.
Dehumidifying equipment and fans have been installed in the basement to minimise the risk of moisture damage to the remaining collection of pamphlets and books, some of which date from 1600.
Christine Wise, development librarian, said: 'As far as we are aware, there has only been minor damage to stock.
'We are removing material from the library so we can take up the floor coverings and dry the room out.
'We are dealing with basic telephone inquiries, although we cannot give a date for when we could reopen.
Mrs Wise said Britain's oldest and largest library devoted to the study of women is actively pursuing plans for a new home, probably purpose-built.
The present location in a damp basement and the lack of resources to pay for upkeep, have both been criticised.
Much of the older material is printed on poor quality paper, and despite the best efforts of conservators the lack of temperature and humidity control has meant parts of the collection were decaying even before Thursday's floods. Access to the more vulnerable items is limited to prevent their further deterioration.
In 1992 curators appealed for pounds 1m to secure the collection's future, and pay for conservation such as transferring material to microfilm.
The Fawcett is administered by the University, which as the City of London Polytechnic took in the collection in 1977 when it was threatened with dispersal.
It is named after Millicent Garrett Fawcett, leader of the women's suffrage movement, who died in 1929. Author of Political Economy for Beginners, Fawcett campaigned for women to have voting rights and higher education.
Her sister, Elizabeth Garrett Anderson, was the first woman in Britain ever to qualify as a doctor.
As well as containing 45,000 books and pamphlets, the library also houses many Suffragette banners, and the archives of the Josephine Butler Society, including thousands of her letters arguing against the white slave trade, and the Contagious Diseases Act, which allowed the police to force women suspected of prostitution to undergo medical inspections.
Janet Grenier, chairwoman of the Friends of the Fawcett Library, said: 'This is the leading women's history library in the country, it is unique.
The flood was a tremendous blow. 'The library is so important and the Friends have raised money for it but there is a lack of proper outside funding, and that is a scandal.
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