The 4m (13ft) whale had been stuck in the river, north-west of Paris, for a week amid growing concerns about its health.
It was removed from the river, with a giant net, on Tuesday night, and transferred to a barge where a dozen vets were waiting to treat it. It was later transferred to a refrigerated truck for transport to a saltwater pool in Normandy where there were hopes it would recover before being released into the sea.
However, just before 11am on Wednesday the team caring for the the whale said it had had to be euthanised after developing breathing difficulties.
Veterinarian Ollivet Courtois said that during the rescue operation, the dangerously thin mammal began to have breathing difficulties, and so experts decided to humanely euthanize the creature.
The whale, which became a local celebrity, was first spotted last week having accidentally veered off its normal path to the Arctic.
The plan had been for the whale to remain in its temporary saltwater home, in the northeastern French port town of Ouistrehamof, for "two to three days" of surveillance and treatment before being towed out to sea, according to Isabelle Dorliat Pouzet, deputy prefect of the town of Evreux.
Beluga Whale rescue attempt - In pictures
"Then, nature will take its course," Ms Pouzet said. "We have to be optimistic... the work has been painstakingly prepared."
Authorities earlier said the move carried risks because of the stress on the animal but, the whale couldn’t survive much longer in the Seine's freshwater habitat.
Drone footage shot by French fire services last week showed the whale meandering into a stretch of the Seine between Paris and the Normandy city of Rouen that is far inland from the sea.
Conservationists have tried unsuccessfully since Friday to feed fish to the beluga.
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