Greenpeace marine biologist Thilo Maack said they had tried to stop the whale entering a shallow bay on Poel Island, but it had done so anyway.
First spotted in German coastal waters in early March, the whale is thought to have become entangled in netting before eventually becoming stranded on a sandbank on Timmendorfer Strand, near the town of Travemünde.
The humpback is also thought to have been suffering from a skin condition brought on by the lower salt levels of the Baltic Sea.
Late last week, hopes had been high that the whale might move to deeper waters after excavators dug a channel enabling him to swim off.
Attempts to guide the humpback towards the saltier waters of the North Sea proved unsuccessful, and he swam some distance east along the coast before becoming stuck again in a coastal bay in the city of Wismar.