The National Capital Authority approved the lake's use as a landing spot for planes from Sydney and the NSW south coast.
Lake Burley Griffin is a popular yachting, wind sailing and rowing spot and some areas are also braved by swimmers.
A proposal for seaplanes to use the lake was first put to the Canberra community for feedback in May.
Sydney Seaplanes proposed a commuter service between Lake Burley Griffin and Rose Bay in Sydney three times a day, while South Coast Seaplanes wants flights between Canberra and the south coast twice a week.
Of 102 public submissions just 21 supported the idea.
Most opposition to the proposals was due to lake users' safety concerns and environmental impacts from noise and pollution.
Yet tourism operators welcomed the idea and said it would bring more visitors to the capital and showcase the city.
The NCA determined any potential impacts of the seaplanes were outweighed by the benefits the proposals had for tourism to the region.
But the NCA acknowledged the safety concerns raised by community groups and said guidelines would be developed for the "shared and safe" use of the lake.
Work on the guidelines is expected to start in February.
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