It made her the most successful athlete of the entire Paralympic Games and Australia's most successful athlete at a single Paralympics.
As well as picking up the Australian Paralympian of the Year prize, Freney also took the Female Athlete of the Year trophy and admitted she was delighted to claim both the prestigious awards.
"It is an absolute honour, I didn't expect this at all," she said.
"To be acknowledged by the Australian Paralympic Committee and know that they are behind me is such a good feeling.
"I knew I'd be up against a tough field of nominees and to have my dedication to swimming acknowledged is phenomenal.
"It's been a pretty busy time since London and I've really enjoyed the post-Games atmosphere.
"All my hard work has finally paid off and to win this award and experience the amazing public support is a wonderful thing."
Elsewhere the Male Athlete of the Year went to sprinter Evan O'Hanlon.
The 24-year-old claimed the 100 and 200 T38 metre gold medals, both in world record times to earn the honour of being Australia's flag bearer at the London 2012 Closing Ceremony.
The Team of the Year prize was awarded jointly to the Australian wheelchair rugby team and sailing's two-person SKUD 18 crew.
The wheelchair rugby team went undefeated as they claimed gold in the final with a 66-51 over Canada while the unlikely pairing of sailor Daniel Fitzgibbon and five-time Paralympic wheelchair basketball player Liesl Tesch combined on the water to win Australia's first sailing gold since Sydney 2000.
Fitzgibbon's strategic sailing skills and Tesch's competitive nature and natural talent were for all to see as the SKUD 18 pair won four of the 10 regatta races and never once finished outside the top three.
The Junior Athlete of the Year prize was also tied between swimmer Maddison Elliott and athlete Rheed McCracken.
At 13-years-old Maddison Elliott was the youngest Australian to ever at a Paralympic Games but surprised many when she won gold in the women's 4x100m freestyle relay, silver in the 50m freestyle and bronze in the 100m and 400m freestyle.
Meanwhile on the track, 15-year-old Rheed McCracken won bronze in the 200m before going one better to win silver in the 100m on the final day of athletics competition, earmarking him as one of Australia's track stars of the future.
Coach of the Year went to cycling head coach Peter Day, who enjoyed one of Australia's most successful Games campaigns ever in Paralympic cycling.
His team of 12 athletes and three sighted pilots combined to win six gold, four silver and four bronze medals, doubling the number of cycling gold won in Beijing 2008.
The President's Medal for Excellence in Sportsmanship from APC President Greg Hartung went to cyclist Kieran Modra and shooter Libby Kosmala.
With 14 gold medals between them, it was a fitting honour for the pair who exemplify the award's values of respect, honour, fairness, modesty and integrity.
Tandem cyclist Modra competed at his seventh Paralympics in London as he remarkably recovered from a horrific car accident in December 2011 to win the 4 kilometres individual pursuit at three consecutive Games alongside sighted pilot Scott McPhee.
Meanwhile shooter Kosmala was competing at her 11th Paralympics and with nine gold medals, she is one of the most decorated and experienced athletes in Australia.
Her love and passion for shooting was evident when, at 70, she became the oldest athlete to compete at the London 2012 and made the final of her pet event in the 10m air rifle standing.
There was also a special presentation for swimmer Matthew Cowdrey, who was honoured after becoming Australia's most decorated ever Paralympian in London.
At just 23, he has won more Paralympic gold medals than any other Australian, putting his name in the record books with 13 golds.
His five gold, two silver and one bronze medal in London took his career total to 22 medals.
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