The century-old Astoria has been owned by the group's guitarist David Gilmour for 28 years and has also been used for his solo material as well as mixing a number of releases.
The Floyd frontman's wife Polly Samson posted a picture of the houseboat online with webbing straps stretched across a flooded riverbank to hold it in position on the deluged River Thames.
She wrote on Twitter: "They've tied Astoria to a tree to stop her from floating away."
The boat - moored at Hampton, Surrey - was built for music hall impresario Fred Karno, whose troupe of comic acts included Charlie Chaplin and Stan Laurel, in 1911.
Its grand scale, at 90ft long, was designed to accommodate an orchestra to enable Karno to have the finest boat on the stretch.
It has been used to record sections of Pink Floyd albums A Momentary Lapse Of Reason and The Division Bell, and also featured in the BBC series Three Men In A Boat, in which Dara O'Briain, Griff Rhys Jones and Rory McGrath recreated the journey in the book by Jerome K Jerome from Kingston Upon Thames to Oxford.