NOT that I live in an area that even has a Waterstone's, but I thought the article was interesting, and then read that your link wouldn't open on your comp, Ruth! Thought I'd try to help. The article SEEMS like it won't be placing every book at $5 (forgive me.. I don't know if we even have 'pound' signs on our comps in the US!), just individual books that are part of a campaign:
The 296-store Waterstone's business is now said to be looking at introducing money-off deals for individual books from September, instead of the blanket three-for-two, either pricing campaign books at £5, or introducing a "staggered" offer for paperbacks at £3, £5 and £7.
Not sure if particular campaigns will run for a month, 2 weeks, 3 months, etc... but regardless, it seems that only certain books will be part of that $5 special. Hope this helps!