Earlier this month, Holman Barnes Group (HBG), which owns a majority stake in NRL side Wests Tigers and shares in NPL NSW football club APIA Leichhardt, stepped in as investors to save the women's team.
The women's and men's teams now have different backers, as Total Soccer Growth Holdings chose to only invest in the A-League Men team when they took over in June, initially leaving the ALW team in danger of folding.
Heffernan coached Western Sydney between 2019 and 2021, leading the Wanderers to their maiden ALW finals series in his first season, then quitting at the end of his second campaign.
The 46-year-old, twice capped by the Socceroos, spent four seasons at the Mariners as a player, including winning the 2007/08 premiership.
"It's a very proud moment to be back coaching at the Mariners," Heffernan said in a statement.
"I had some of the best years of my playing career here, and I'm incredibly excited about the opportunity to create some special memories again - this time as a coach."
Heffernan replaces Kory Babington, who departed when the Mariners' future looked uncertain and has since become an assistant to Leah Blayney at Calgary Wild.
"It's a major coup to have Dean back," women's football boss Matteo Maiorana said.
"We are trying incredibly hard to ensure the Mariners women's team is a team that the whole Central Coast community can get behind and support.
"Having someone who is so deeply embedded in the fabric of the club, who knows what wearing that yellow and blue jersey means, was integral as we establish the team within our new ownership structure.
"Putting aside his history with the club, Heff is a fantastic coach."