The Gudang Yadhaykenu, Atambaya and Angkamuthi peoples took control of 362,000 hectares of land in a ceremony at Injanoo on Wednesday, eight years after they were granted Native Title rights by the Federal Court.
The lands handed over include the former Jardine River National Park, Denham Group National Park and two offshore islands.
Angkamuthi elder Sandra Woosup says the handover comes after a 27-year fight spanning generations of the three groups.
"I don't know what to say, like it's really a blessing for us today now, to see this finally come to us, giving land back," she told reporters in Injanoo.
Gudang Yadhaykenu elder Nicholas Thompson-Wymarra says his people can revive their culture more than 100 years after Europeans took over their country.
He said regaining ownership over the waters is particularly important because the Rainbow Snake is a central figure in Gudang Yadhaykenu culture.
"We're the saltwater and freshwater river people, and as sand beach people, you know, it's been great to be able to have the opportunity to revive our dreaming again, and for who we are and our identity," Mr Thompson-Wymarra told reporters.
"And who we are, as we are, has been lost for many decades due to the past dark history that's happened here."
Premier Annastacia Palaszczuk said handing back the land was something "we deeply believe in our hearts is right".
She said First Nations peoples had suffered atrocities in the past, but they would now be able to take control of their futures.
"It is in part a painful history and I echo the earlier words and acknowledge the courage and resilience demonstrated by your ancestors," the premier said in a speech.
"I acknowledge the courage and resilience continued by the current generation, which ultimately led us, to our government, returning these lands to you.
"But we must never, ever forget the past."
The three groups have signed deals to grant part of the lands to two new protected areas: the Apudthama National Park and the Yamarrinh Wachangan Islands National Park.
The two parks will be jointly managed by the Ipima Ikaya Aboriginal Corporation, representing the three groups, and the state government.
Ms Woosup took the opportunity to warn Metro Mining, which plans expand its existing bauxite mine on her traditional lands, that the Angkamuthi people opposed all mining.
The Angkamuthi people would prefer to manage their owns lands, Ms Woosup said, rather being pressured to allow mining projects.
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