A deal between the US online retailer and the UK bookstore chain will also see Waterstones “launch new e-reading services” alongside the devices.
Waterstones was widely expected to reach a deal with US retailer Barnes & Noble to sell its nook ereader.
WHSmith, the biggest high street rival to Waterstones, has a similar deal with Canadian-based Kobo.
In a statement Waterstones MD James Daunt said: “It is a truly exciting prospect to harness also the respective strengths of Waterstones and Amazon to provide a dramatically better digital reading experience for our customers.”
“The best digital readers, the Kindle family, will be married to the singular pleasures of browsing a curated bookshop. With the combination of our talents we can offer the exceptional customer proposition to which we both aspire.”
Jeff Bezos, Amazon.com Founder and CEO, said: “Waterstones is the premier high street bookseller and is passionate about books and readers – a dedication that we share deeply. We could never hope for a better partner to bring together digital reading and the physical bookstore.”
The companies say further details will be released “in the autumn”.