With a growing economy, increasing population, and climate change, Canada faces increased pressures on its precious resource: freshwater (20% of the world’s freshwater). Current methods for monitoring the health of our watersheds remain slow, laborious, expensive and imprecise. Canada’s geographic diversity and low population density makes monitoring networks a challenge to maintain. We need more efficient, comprehensive monitoring tools to inform governments, communities and industries about the true consequences of economic development on freshwater quality, to support rapid and effective protection of vulnerable ecosystems. The WWF- Canada and Environment and Climate Change Canada (ECCC) are working with Dr. Mehrdad Hajibabaei of the University of Guelph to validate and implement a new technique called environmental DNA metabarcoding, which uses bulk environmental samples for identification of species through species specific genomic sequences (DNA ‘barcodes’) using high-throughput sequencing technologies. The project will generate biodiversity data for freshwater benthic macroinvertebrates, the small animals that live at the bottom of streams, rivers. The technique will be used to analyze bulk samples collected by community-based monitoring efforts across a wide range of Canadian watersheds. Sampling by community groups will be coordinated by WWF-Canada and its partner organizations such as Living Lakes Canada. Implementation at this scale will be a world first, supporting the wider adoption of these technologies within existing environmental monitoring and assessment applications, including ECCC’s Canadian Aquatic Biomonitoring Network (CABIN) which engages over 1,400 users, including federal, provincial and territorial government agencies, First Nations, academia, industry, NGOs and environmental consulting firms. Many of these organizations already use biomonitoring to understand and manage the impacts of resource projects such as mines, hydro dams and energy projects. By providing access to this new genomics-based technique, and by demonstrating its reliability in assessing river health, we can broaden the reach and impact of existing community-based monitoring programs, ultimately leading to better informed decisions.