Freshwater fish resources contribute to Canada’s economy both directly and indirectly. Thriving freshwater fish resources are the lifeblood of many rural, northern and Indigenous communities and are central to the social and cultural lives of millions of Canadians. Yet, freshwater fish stocks are under threat. Canadian freshwater fish stocks need science-based monitoring and management. The logistical difficulties of monitoring fish stocks in Canada’s 2+ million lakes and countless rivers are compounded by the limitations of conventional sampling methods, which provide only a snapshot. The project will use genomic approaches to develop a Fish Survey Toolkit based on environmental DNA from water samples and a Fish Health Toolkit that will provide quantitative assessments of the health of fish and the stressors they face. Collectively, these toolkits will enable a complete and accurate assessment of the status of Canada’s freshwater fish resources and save millions of dollars for government, NGOs, fish culture facilities, and environmental consultants in fish survey costs, and will result in additional indirect savings through more effective and directed management actions. Furthermore, and most importantly, the project will ensure sustainability of Canada’s freshwater fish resources for generations to come.