It is believed the adventurous seal swam up the Great River Ouse from King's Lynn, Norfolk, and then glided into the nature reserve through the high flood waters.
Graham Elliott, area manager for the RSPB, said: "It would be the first time this has happened to my knowledge that one has made its way into the lake.
"The floods normally come from ground water rather than the river and so if there is one it must have worked its way up in a ditch or something like that.
"It would be tremendous if one is there. It would be extremely unusual and it would become an attraction to visitors."
Wildlife workers said seals had occassionally been spotted in the nearby River Great Ouse but only ever as far inland as Earith.
To reach the lakes at Fen Drayton the seal has travelled ten miles further than the areas where they can be spotted.
Mr Elliott added: "I am not entirely sure where the video was taken from, but it looks to me as though it may have been taken across the river from the Holywell side and the animal is entering the lake known as Ferry Lagoon.
"The water levels are amazingly high and the whole site is flooded."
