The store said it would be closed for trade and unable to immediately respond to phone calls and emails but customers could still order books online.
"The great floodgates of the wonder-world swing open," staff wrote on a notice, quoting Herman Melville's great American novel Moby Dick.
"We'll be doing our utmost best to be back on our feet as soon as possible, soggy but unbroken," the company said on its Facebook page.
The shop is well-known in Wellington for holding free literary events and book launches, including the release of Nicky Hager's Dirty Politics book last year.
Unity Books manager Tilly Lloyd told Radio New Zealand it was not clear whether the sprinkler was automatically deployed or whether a pipe burst, but the water ruined hundreds of books and shut down the shop's phone and computer systems.
