Minister for Water Resources David Littleproud said the $6.5 million dollar investment would make sure people drawing from the Basin had secure water for generations to come.
"This will take the guesswork out of managing water in the Basin," Minister Littleproud said.
The Basin still holds many mysteries such as how water naturally flows beneath the earth.
"This is the water that keeps the outback running and we've got to make sure it lasts," he said.
"More than 180,000 people living in the outback depend on its water, along with 7,600 businesses worth $13 billion a year.
"This project will tell us how water enters the Basin from rainfall, how it is used and how much is held in storage."
Geoscience Australia will measure gravity changes across the basin which will be analysed by supercomputers.
"We'll also be using the knowledge of industry and geologists who have worked in the Basin," Littleproud said.
"What we learn will help us make important decisions balancing long term social, economic and environmental outcomes."
The project is in addition to the government's $36.9 million drought resilience package in the Great Artesian Basin to improve water security by capping leaking and replacing open channels with piping.