The female Northern Bottle-Nosed Whale was first spotted last Friday near the Houses of Parliament, some 40 miles (65 km) from the sea. It died on Saturday evening after rescue teams failed in an effort to return it to open sea.
"A combination of factors was likely to have been the cause of the death and these factors include severe dehydration, some muscle damage and reduction in kidney function," said the Zoological Society of London (ZSL) in a statement.
It said that anti-submarine sonar signals -- which some media reports suggested had possibly confused the animal -- were unlikely to have contributed to the death.
The ZSL said the most likely scenario for the 18-ft (six metre) whale is that it entered the North Sea off eastern Britain by taking a wrong turn above Scotland.
Subsequently it tried to head west to where it belonged in the east Atlantic by swimming up the river.
"The death of a bottlenose whale in the Thames from dehydration ... confirms our thoughts that the whale drove itself into the shallows of the river because it was feeling unwell and had become disorientated," said Leah Garces, campaigns director at the World Society for the Protection of Animals (WSPA).
ZSL veterinary pathologist Paul Jepson, who carried out the autopsy, said early blood tests had shown the whale was remarkably free of parasites or any disease. There was also no evidence that the animal had any internal injury.
Tests were continuing, he told reporters.
He said the last few days had been an unforgettable and ultimately sad experience.
"We are now determined that the whale did not die in vain ... the incident has demonstrated a clear message of the nation's passion for these animals and their conservation," he said.
The WSPA's Garces added: "Across the world, more than 2,000 whales are hunted and killed each year through inhumane 'scientific' and commercial whaling by Norway, Iceland and Japan."