The animal was spotted first Friday by a local, who had been trying to help it along.
More locals joined the rescue effort Saturday when it was spotted again, pouring water on it to keep it hydrated.
Bernadette Matthews was one of the residents who tried to keep it alive.
"Even swimming with him, we weren't able to hold on to him and he got away and today he was spotted," Matthews said.
The turtle was about 20 kilometres up the river, a long way from the salt water, which it needs to live.
The nearest body of salt water is the Bay of Fundy.
On Sunday, officials from the Department of Fisheries and Oceans removed the animal from a mud flat, using a winch, ropes and chains.
A male leatherback turtle can reach a weight of 900 kilograms — about 2,000 pounds — according to Fisheries and Oceans.
They're the largest reptile in the world, and are designated as an endangered species under the International Union for Conservation of Nature.
The Canadian Sea Turtle Network Initiative says the waters off Canada's East Coast support the highest concentration of leatherback sea turtles in the north Atlantic Ocean.
They're sometimes seen at the ocean's surface looking to feed on jellyfish.
"Everybody tried to keep it as wet as possible but what can you do, there's no jellyfish in this river, it didn't work out, it wasn't its day," said Heather Burke.
The male turtle, which was estimated to be about 272 kilograms, or 600 pounds, will be sent to Charlottetown for a necropsy, according to DFO.