Some survived on Arks. Righteous folk, craftsmen and preachers, they bought liners or restored hulks or commandeered the vast merchant ships into floating sanctuaries - taking with them animal and plant life to sustain themselves.
The peaks of mountains could be found among the waves, where life on solid ground could flourish again. Pristine islands, where humans could live peacefully and in harmony - with nature and themselves. Or, as the case may be, in no kind of harmonay whatsoever. These paradises swiftly became known as Edens.
As the waters rose and the kingdoms of men were swept away, all thought that those not in the Arks or on the Edens had been lost. But it was not to be.
The ancient cities of the world, filled with sacred architecture and seated at the nexuses of lay-lines somehow rose up, despite their freight of unrepentant souls and festering sin. With ragged edges, fringes of seaweed and wave-washed streets they re-emerged, with much of their population undrowned. They do not float or bob like any natural material but they stay, somehow, atop the waves. But what is more, they have protectors.
Ancient spirits or new icons pull these through new seas. Rome is propelled by a doggy-paddling She-Wolf. Gog and Magog pull London by great chains - largely in the same direction. Cairo rides gracefully upon the crinkled hide of a giant crocodile. New York rejoices as it shelters behind the sea-weed skirts of Mother Liberty, her torch permanently grounded at Battery Park. Her course is assumed to be determined by public vote. The spirit of Mother Ganga moves Kolkata; her half-elephant steed Makara pulling the city across seas wider than any river.
In these cities, old ritual draws up new powers; miracle workers of the new age, the mystery cults of the city fathers, slum prophets and sorcerous advisors. The shattered science of the drowned world is put to use for new causes; vast profit and power can be found by freelancers and small operators. A time for adventure - and the possibility of escape from the befoulled remnants of the old world...
Equal parts Mortal Engines, The Scar and Leviathan (or, if you prefer, HMS Apollyon). A touch of the swashbuckling and Biblical horror of Raiders of the Lost Ark is also thoroughly relevant.