When the Doctor is talking to Adelaide, he talks about this situation is like trying to save Pompeii, but by doing it he causes the catastrophe. In "Fires of Pompeii" the Doctor fires up mount Vesuvius to save planet Earth, destroying Pompeii.
Russell T. Davies considered drawing on a rejected concept for the 2008 Christmas special in which the world would be transformed into a fantasy landscape drawing upon the imagination of J.K. Rowling - by having the aliens engage in an otherworldly festival on the time-stopped Earth. The story would end with an Ood appearing to the Doctor, beckoning him to return to its planet; this would presage the Doctor's regeneration in the final special.
Adelaide was originally a Russian named Valentina Kerenski, with Helen Mirren written in mind. Russell T. Davies feared that this was too similar to Mirren's turn as Tanya Kirbuk in 2010 (1984). She was renamed Grace, then Adelaide.
This story was initially envisaged as a Christmas special. Several festive references remain, such as the crew on Mars preparing for Christmas dinner, and the snowing when the Doctor arrives back on Earth as he exclaims how he likes snow.
Phil Ford envisaged Mars in the adventure as a terraformed planet, with the Bowie base personnel flying great distances to various installations. Russell T. Davies encouraged him to take a much more low-tech approach to the story, with Bowie Base as the rugged first outpost on the untamed Martian frontier.
The service robot was inspired by WALL·E (2008). The original plan was for the robot would initially be clunky yet lovable, but might later go mad and become a threat to the Doctor. This aspect of the character ultimately went unused.
Phil Ford's original draft was called A Midwinter's Tale, and was a sword and sorcery tale about an alien princess coming to Earth to be married. It ended with a long chase sequence in secret tunnels beneath Buckingham Palace.
Russell T. Davies originally had an idea in which the Earth is frozen in time due to an alien presence. Much of the action would be based around a hotel, which would suddenly be empty except for one human who would become the Doctor's temporary companion. Originally, Davies had envisaged this as a father who would be driven to assist the Doctor by his desire to be reunited with his missing family. However, he was eager that one of the surrogate companions be a strong older woman - who might be played by an actress of the calibre of Judi Dench or Helen Mirren - and so this character instead became a grandmother.
The trivia items below may give away important plot points.
Some clever fans worked out that the letters in the title, The Waters of Mars, can be rearranged to form "Wars of The Master", which led to the prediction (correctly) that this was a hint to a return of The Master in Doctor Who: The End of Time: Part One (2009).
The original draft of the script had Adelaide surviving, with the Doctor realising upon seeing Ood Sigma (who arrived straight after he'd declared himself the 'Time Lord Victorious') that he had gone too far.