Organisers had hoped to raise $500,000 through the auction of 45 works donated by a number of well-respected Aboriginal artists.
All the paintings sold, and one raised $140,000 in bidding.
Paul Sweeney from the Papunya Tula Arts Centre in Alice Springs said he is thrilled by the result.
Mr Sweeney told the ABC that the money will be spent towards pools in the Maningrida and Kintore communities.
He said it is important for Aboriginal children to have access to the benefits of swimming pools.
"Apart from being somewhere the kids can go in the middle of summer when it's over 40 degrees for a swim after school, it'll also be contributing to the health of the community, which is a very important issue as well" he said.
"We will need a little bit over a million dollars for each community to build the pool so if you divide that up, we've gone halfway, which is a pretty big contribution," he said.
The Kintore community, 500 kilometres west of Alice Springs, has no pool, and kids there reportedly often resort to swimming in sewerage ponds to cool down.
"Aboriginal children in those communities are at high risk, they often exploit very unsuitable and often dangerous alternatives to swimming in a pool, and that might be swimming in sewerage ponds, swimming in crocodile infested waters, and so on," said Hetti Perkins, curator of Aboriginal and Torres Straits Islander Art at the gallery.
She said there are reports of children drowning while swimming at road excavation sites and stock watering holes, and are often vulnerable to things like box jellyfish.
"You can imagine how exposure to that sort of environment only exacerbates the health issues that are facing these children already such as skin infections, eye infections, ear infections, and so on," she said.
Evidence suggests that swimming pools help lower the incidence of infections and other health issues like perforated ear drums, all of which are common in indigenous communities.
A swimming pool built in Wadeye, also in the Northern Territory, has not just given local kids a place to cool down and chill out, it's helped reduce infections and lower school truancy rates, thanks to a "no school, no pool" policy.
A similar auction in Sydney five years ago raised nearly a million dollars, enough money to buy a dialysis unit for the Kintore community.
The auction was held on the fortieth anniversary of the Freedom Rides, which sought to give Aboriginal children access to public swimming pools.