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Baker, who is based in Queensland, was second to 2009 world champion Melissa Gorman who dominated the 10km women's race, winning by nearly five minutes.
Baker broke free from a four-strong chase group over the final kilometre to claim second in 2 hours 03 minutes 55 seconds.
She finished provisionally inside the qualifying process for July's world championships in Shanghai where the top-10 finishers will earn direction selection for the 2012 London Olympics.
Swimming New Zealand Open Water manager Phillip Rush said Baker impressed, although she had swam conservatively with the vital world championship selection at stake.
"Cara wanted to make sure she qualified for Shanghai and probably swam within herself today. I really believe, if she puts in the hard work in the next couple of months, that she has the potential to finish in the top-10 at the world championships,"Rush said.
"Gorman's swim today was world class and she will be the likely gold medal favourite for Shanghai. And if Cara swims to her potential, she can match Gorman's speed."
Meanwhile Rotorua's Kane Radford was the best of the New Zealand men, finishing in seventh place in 1hr 55min 58secs.
New Zealand swimmers had to finish in the top four or within 20 seconds of the winner to qualify for the world championships.
Women: Melissa Gorman (QLD) 1:59.03, 1; Cara Baker (New Zealand) 2:03.55, 2; Danielle DeFrancesco (QLD) 2:04.02, 3. Also Bridget Maher (NZL) 2:19.40, 11.
Men: Ky Hurst (QLD) 1:55.04, 1; Rhys Mainstone (QLD) 1:55.05, 2; Trent Grimsey (QLD) 1:55.10, 3.
New Zealanders: Kane Radford 1:55.58, 7; Phillip Ryan 1:57.44, 13; Casey Glover 1:59.48, 14; Jon Pullon 2:02.13, 19; Andrew Pullon 2:09.26, 24.