The Doctor asks the Silurian scientist if he has any celery. This refers to the habit of the Fifth Doctor, who always wore a sprig of celery. The celery was a cure for several poisons that affect Time Lords.
The actors portraying Silurians in previous stories didn't wear masks. The masks here helped save time and money since the actors wearing masks didn't require as much time in make-up.
Chris Chibnall wanted to give the the episode a distinctive feel by changing the principal setting: after focussing on the human community of Cwmtaff in The Hungry Earth (2010), the underground Silurian city would predominate this episode.
The first time the Doctor met the Silurians their hibernation was disturbed by the construction of a particle accelerator deep beneath the earth's surface.
Amy and Mo's discovery that the Silurians have kidnapped a menagerie of modern animals, including a dog owned years earlier by Tony Mack was cut for time.