Walkers found the man's body on Saturday afternoon in a stream near the small town of Neu Darchau in Lower Saxony. His appearance and personal items identified him as belonging to the anti-nuclear demonstrations, a police spokesman said.
It appeared the man slipped and fell into the stream while urinating, the spokesman said.
On Monday afternoon police said the man was a 47-year-old from Mainz. He had not been reported missing.
Police found his identity by comparing his fingerprints to those in their criminal database. He had been arrested for disturbing the peace, though police did not reveal where or when.
Earlier this month, thousands of demonstrators blockaded the shipment of 123 tonnes of nuclear waste to the controversial Gorleben nuclear waste depot.
A massive force of about 20,000 police was needed to clear the road for the 20-kilometre journey to the storage site after it had been processed in France and then brought back to Germany by train.
The demonstrators, including farmers with tractors, blocked approach roads to the storage facility.