The Ekati mine has a waste management plan to reduce, reuse, recycle, and responsibly dispose of the waste it generates.

In 2015, more than 3.67 million tonnes of kimberlite ore were processed in the process plant and more than 18 million tonnes of waste rock (mined rock that does not have economic value) were deposited into waste rock storage areas. Coarse processed kimberlite material was used as landfill cover, while fine processed kimberlite, mine sump water, treated sewage, and process plant effluent were deposited into the Long Lake Containment Facility. Fine processed kimberlite was deposited into Beartooth pit.

Most water used at the Ekati mine is sent to one of two containment facilities – these are lakes that hold water used in mine activities until the suspended solids can settle and the clean water can be released back into the environment. The majority of mine water goes into the Long Lake Containment Facility. Water from that facility is then discharged into Leslie Lake. Mine water is also deposited into the King Pond Settling Facility and later used to suppress road dust. Prior to discharge, water quality must meet the criteria set in the water licence.

Hazardous waste such as oily rags, aerosol cans, waste grease, oil, and fuel filters is collected and sent off-site where it is combined with similar waste from other facilities.