The dual Olympian replaces Barclay Nettlefold, who resigned in June after just eight months in the job when he was accused of making an inappropriate remark to a female team consultant.
That was just one of a string of negative incidents that have dogged the body since the swimming powerhouse slumped to its lowest Olympic medal haul in 20 years at last year's London Games.
Bertrand was skipper of Australia II when it won the America's Cup in 1983, ending 132 years of United States dominance of the yacht racing challenge and sparking nationwide celebrations.
"I've had an association with high performance sport and high performance teams for more than 40 years and this appointment is one of the highlights of my career," the 66-year-old said.
"Swimming has a proud history in this country and a reputation for hard work, humility and success. This tradition needs to continue and be a clear focus for all athletes and coaches as we head towards (the) Rio (Olympics) in 2016.
"Australians love watching our gold-capped swimmers in action and personally I get a real sense of pride when they are making their presence felt on the swimming world stage."
Betrand takes over an organisation still reeling from a scathing review into the London Games in February which said poor management had allowed a "culturally toxic" environment to develop with abuse of alcohol and prescription drugs, as well as flouting of curfews and bullying going unchecked.
Six top swimmers, including 100 metres world champion James Magnussen, were subsequently fined for taking Stilnox, a sedative banned by the Australian Olympic Committee, as part of a 'bonding' session in the lead-up to London.
An Independent Swimming Review into the high performance programme commissioned by the Australian Sports Commission also reported in February, making 35 recommendations for improvements.
Swimming Australia was also hit in the pocket with the withdrawal of a major sponsor and only last week, an AOC report into the Stilnox incident slammed the body for failing to report it to the Olympic team hierarchy.
"My immediate focus will be to provide the corporate leadership and direction to ensure continued improvement in sporting results, corporate governance, team culture and grass roots growth at the community sport level," Bertrand added.
Major changes have already taken place with head coach Leigh Nugent resigning in March and a new chief executive, Mark Anderson, and high performance chief, Michael Scott, being appointed in April.
"I look forward to partnering with John as Swimming Australia continues to take some important next steps and build upon the positive progress the sport has already made this year," Anderson said.
"We will work together and with all our key stakeholders to ensure swimming in Australia is once again a formidable powerhouse on the world stage."