I can't recall the exact wording, but there was a (written) message at the end of the last episode to the effect that there will be a third series of Merlin.
The episode ended with 'Merlin will return". So, they finally planned the 3th one ?
Yes, confirmed by a BBC press release, on December 3rd:
BBC - Press Office - Merlin commissioned for new seriesHit family fantasy drama Merlin, produced by Shine Television, has been recommissioned for a third series for BBC One.
The announcement comes as the second series of the Saturday-evening show continues to enthral audiences, pulling in a peak of over six million viewers and a 31% share.