Director Sam Fell conceived the idea of rats falling in love in the sewers while working on Aardman's Chicken Run (2000), and developed it into a story with producer Peter Lord before pitching it to DreamWorks in 2001.

Producer Peter Lord described the film's pitch as 'The African Queen with the gender roles reversed.'

The film was originally announced in 2002 under the working title Ratropolis, before comedy writing duo Dick Clement and Ian La Frenais were brought on to write the script.

Flushed Away was Aardman Animations' first project made entirely in 3D CGI instead of their traditional stop-motion claymation, because using water on plasticine models would damage them and compositing CGI water into live clay shots would have been too costly.

Despite grossing $178 million worldwide, the film's $149 million budget led to an estimated $109 million loss for the studios, a failure that caused Aardman to end its collaboration deal with DreamWorks after three co-productions (Chicken Run, Wallace & Gromit: The Curse of the Were-Rabbit, and Flushed Away).

The film won five of its eight nominations at the 34th Annie Awards, including Best Writing and a Voice Acting award for Ian McKellen's performance as the Toad.

A tie-in video game released alongside the film for PlayStation 2, GameCube, Game Boy Advance and Nintendo DS received negative reviews from critics despite winning an Annie Award for Best Animated Video Game.