Across Canada there has been movement towards the adoption of principles of collaboration in water governance which should in principle be more supportive of meaningful co-governance roles for Indigenous peoples. While the meaningful engagement and involvement of Indigenous peoples in decision-making has been recognized as a necessary precondition of collaborative water governance, its realization in practice has been limited. By exploring the policy process during the development and implementation of the Great Lakes Protection Act, 2015 in Ontario, this paper explores the strengths and ongoing challenges of engagement processes between First Nations and colonial government in Ontario’s water governance system. Ongoing challenges that are preventing the realization of true co-governance with First Nations in Ontario’s water system are identified, including: capacity challenges, limited recognition of First Nations as rightsholders, challenges with knowledge sharing, limited engagement with First Nations at a strategic level and challenges in developing trusting relationships, amongst others. While there are indications that the relationship between First Nations and colonial governments in Ontario is moving closer towards principles of co-governance, meaningful shared governance will not be achieved without substantial learning for all parties and shifts in power structures.