In the sci-fi drama's mid-series finale, it was revealed that River (Alex Kingston) is the daughter of Amy Pond (Karen Gillan).
"I used the name Pond for that reason, to create a link," Moffat told TV Guide. "[That reveal] was Plan A for a long time."
He added: "My favourite dirty joke in Doctor Who is the title of episode 13 in series 5, 'The Big Bang', [because it's] the night when River began. I laughed a lot when I thought of that."
Moffat also insisted that the familial link between Amy and River "makes sense" when looking back at past episodes.
"I think that the moment that you actually see them together [you notice] how similar they are in certain aspects," he suggested. "That sort of devil-may-care attitude, how naughty they are. Either of them, without the presence of The Doctor, would just be wicked."
Karen Gillan previously said that she is looking forward to exploring River and Amy's changed relationship.
"That's going to be really fun, considering... the big revelation," she said. "We'll see parental instincts coming into play."
Doctor Who returns to BBC One this Saturday at 7.10pm and airs the same day at 9/8c on BBC America.
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Watch Karen Gillan discuss the return of Doctor Who with Digital Spy below: