The consequences of polar amplification of warming include a longer ice-free season leading to increased evaporative stress on lakes, and reductions in winter precipitation that can lead to reduced snowmelt contributions to lakes and rivers. Water quality is also a fundamental concern due to exponential growth of northern communities, and resource development activity intensifies. The confluence of climate change and development pressures has led to several northern communities voicing strong concerns over the sustainability of local fisheries as well as identifying looming water crises. Since water governance systems in northern Canada are under rapid evolution, we examine key vulnerabilities from both a human-centered perspective, as well as the biophysical evolution of freshwater systems in response to a warming climate. This requires working in partnership with indigenous peoples, and incorporating indigenous knowledge and governance structures directly into the research plan.