The exterior of the pirate ship was filmed at a dock in Cornwall, while the lower decks were built from a set at the studio. The principal challenge to film at the dock was to ensure the audience would not see it. The crew set up smoke machines to simulate fog. To create the storm the crew used wind and rain machines, the latter of which went through 15,000 litres of water.
Pirates and "the black spot" as an indication of judgment and doom is a literary device invented by Robert Louis Stevenson. In the 1883 novel "Treasure Island" Billy Bones and Long John Silver both receive a black spot.
This episode takes place in 1699.
This episode was supposed to air in the autumn half of the series, but was swapped around, along with "The Doctor's Wife" being fourth instead of third and "Night Terrors" being ninth instead of fourth. This was because Steven Moffat felt "Night Terrors" was too dark.
The working title for this episode was The Siren.