There is a long history in Canada of Indigenous peoples remaining on the outside of water governance, despite widespread agreement that environmental governance should include all affected parties. The importance of reconciling relationships with Indigenous peoples has launched a number of legislative attempts to improve their involvement in governance, however significant challenges remain. This is true for the Mackenzie River Basin, a transboundary watershed with a diverse and dispersed population. While water governance of the Basin has involved provincial and territorial jurisdictions, the extent of Indigenous participation has yet to be determined. Through a content analysis of the Master Agreement and the 2015 Bilateral between the NWT and Alberta and semi-structured interviews, this study investigates how Indigenous peoples and their perspectives have been represented in governance. Findings suggest that current governance continues to filter Indigenous perspectives through government and fails to achieve a nation-to-nation relationship.