Call Back: In the pilot episode Merlin says of Arthur: "I said you were a prat, I just didn't know you were a royal one." In the final episode of the first series, on saying goodbye to Arthur, they have the following exchange:
Arthur: You know, sometimes I don't think you know who I am.
Merlin: Oh, I know who you are. You're a prat. And a royal one.
- Arthur and Gwen's conversation at the end of 3X10 is filled with allusions to the one they had at the conclusion of 2X02; particularly repetition of the words: "when you/I am King, things will be different."
- In 2x04, Merlin tells Arthur that everyone can see his feelings for Gwen and that even a "blind man could see it." Morgana repeats a similar line to Arthur in 3x10.
- Merlin giving Morgana flowers in 2x03 and later in a deleted scene in 3x01.
- Merlin's conversation with Morgana in 3x07:
Morgana: Why are you telling me this?
Merlin: Because I don't understand why anyone would want to hurt their friends.
Morgana: No, you just poison them.
- In 1x13, Morgana pulls Merlin behind a pillar to warn him about Arthur being in danger. In 3x02, Morgana pulls Merlin behind a pillar once more, but only to threaten him not expose her villainy by reminding that Uther would have him executed if she revealed to him that Merlin poisoned her.
- In 2x12, Morgana recalls to Morgause her assassination attempt on Uther in 1x12.
- Merlin and Arthur's conversation on horse in 4x01 alludes to 2x01:
Arthur: Yes, that you're a clotpole.
Merlin: That's my word.
- In 4x05, Queen Annis says with almost reluctant admiration "There is something about you, Arthur Pendragon..." which seems very reminiscent of something Arthur himself to Merlin in 1x01.
- On the same note, Arthur's line in 1x01 was "There's something about you, Merlin." Perhaps coincidentally, Gwen delivers the exact same line to Merlin in 4x08.
- The scene where Gwen sentences her servant to death mirrors the scene where Gwen is dragged before Uther.
- At the end of 3x02, Uther presents Morgana to the court as the person who turned the tide of the battle and saved Camelot, causing everyone present to applaud her bravery. Morgana was, of course, the traitor who initiated the whole thing. Episode 5x07 ends with Arthur congratulating Gwen for rooting out the traitor who had been trying to kill him (she was, of course, the traitor.) The episode ends with the court cheering "Long live the Queen!"
- In 2x13, Arthur advises Merlin with "No man is worth your tears", to which Merlin replies "You're certainly not". In the Grand Finale, Merlin breaks down when Arthur is dying and Arthur tries to calm him.