The project is expected to create 700 jobs during the construction phase, and 400 jobs on commencing operations.
De Beers Canada CEO Tony Guthrie said: "This is another important milestone for Gahcho Kué and we want to thank the Minister for his review and approval of the water license in such an efficient manner.
"The Gahcho Kué Mine represents a significant investment which will result in employment and business opportunities that will contribute to the economic growth and prosperity of the Northwest Territories."
In August, the project received Type A land use permit from the Mackenzie Valley Land and Water Board (MVLWB).
De Beers will operate the Gahcho Kué project in which it holds 51% stake, while Mountain Province Diamonds holds the remaining share.