Waters's second book, Affinity was published a year after her first, in 1999. The novel, also set in the Victorian era, centres on the world of Victorian Spiritualism. While finishing her debut novel, Waters had been working on an academic paper on spiritualism. She combined her interests in spiritualism, prisons, and the Victorian era in Affinity, which tells the story of the relationship between an upper middle-class woman and an imprisoned spiritualist.
The novel is less light-hearted than the ones that preceded and followed it. Waters found it less enjoyable to write. "It was a very gloomy world to have to go into every day," she said.
Affinity won the Stonewall Book Award and Somerset Maugham Award. Andrew Davies wrote a screenplay adapting Affinity and the resulting feature film premiered 19 June 2008 at the opening night of Frameline the San Francisco LGBT Film Festival at the Castro Theater.