The discovery brings hope to the drought-hit region, tweeted Environment Minister Judi Wakhungu.
The Lotikipi Basin Aquifer was found using satellites and radar.
Last year, scientists released a map detailing the vast reservoirs which lie under much of Africa.
Another aquifer was found in Namibia – the continent’s driest country.
Turkana is one of the hottest, driest and poorest parts of Kenya and was hit by a devastating drought last year.
Many of the region’s inhabitants are nomadic herders, who are especially vulnerable to a lack of rain.
Test drilling confirmed there was water under the ground.
The discovery was announced by Ms Wakhungu at a meeting of the UN Educational, Scientific and Cultural Organization, Unesco.
“This newly found wealth of water opens a door to a more prosperous future for the people of Turkana and the nation as a whole. We must now work to further explore these resources responsibly and safeguard them for future generations,” she said.
The aquifer is said to hold some 200bn cubic metres of water.
According to Unesco, about 17 million of Kenya’