It means the veterans will remain with Trent Robinson's outfit in the eastern suburbs of Sydney until at least the end of the 2024 season.
The signing of Leniu is yet to be confirmed.
It had been heavily reported that both Waerea-Hargreaves and Tupou could have been in line to move on from the Roosters after the moves, despite their long careers in Bondi.
The pair re-signing join a long list of players who have recently committed their future to the Roosters in Egan Butcher, Victor Radley, James Tedesco and Sam Walker, while Joseph Suaalii will also be at the club through to the end of 2024 before heading to rugby union.
Roosters 2024 Player Movements
The moves also leave a short list of off-contract players with first-grade experience, and it's unclear where the Roosters may choose to focus their attention next.
A New Zealand representative prop with 33 Tests under his belt, Waerea-Hargreaves has played 281 games with the Roosters since joining in 2010, and said the club was his home.
“This is my home. It's an honour and a privilege to wear the Roosters jersey, and I consider myself incredibly fortunate to know that I'll continue to be part of the team we have here,” said Waerea-Hargreaves in a club statement.
Meanwhile, Tupou, who has played ten State of Origins for the Blues and is the Roosters' second-highest try-scorer of all-time said he was looking forward to continuing to represent the clubs.
“I cherish every opportunity I get to represent the Sydney Roosters. I love this club and the people in it,” Tupou said in a statement.
“I'm excited about what's ahead and look forward to continuing to work hard and play my role within the team."