The juvenile common seal had been in Ferry Lagoon near Swavesey, Cambridgeshire, for "a couple of weeks", the Cetacean Strandings Investigation Programme (CSIP) said.
Its body was recovered from the edge of the lagoon, adjacent to the River Great Ouse, after it died on 1 March.
The CSIP said a post-mortem examination would be carried out on the animal's body to establish the cause of death.
Common seals are normally found on islands, rocky shores and cliffs, and are particularly common around western Scotland and the northern UK islands.
Rob Deaville, project manager at CSIP, said seals were not normally resident so far inland, but had occasionally made their way up river streams in the past, including the River Great Ouse.
In 2013, a seal was filmed "hopping" into a lake in nearby Fen Drayton Lakes Reserve.
Mr Deaville said he recommended if people spot seals far inland, they should contact British Divers Marine Life Rescue, whose marine mammal medics can monitor the situation and act appropriately where needed.
The body of a young seal has been found in a lagoon 60km (37 miles) inland.