Using environmental DNA to identify emerging Pacific salmon habitats and support Indigenous governance

Northern watersheds are facing rapid hydroclimatic reorganization driven by climate warming, glacier retreat, and intensifying land use. These changes are altering the distribution and accessibility of aquatic habitats, creating both risks and opportunities for cold-adapted species such as Pacific salmon (Oncorhynchus spp.). Effective responses require monitoring approaches capable of detecting contemporary habitat use, as well as emerging or intermittent occupancy in remote and rapidly changing landscapes where conventional monitoring is constrained. Here, we evaluated a species-targeted, quantitative polymerase chain reaction-based, environmental DNA framework using paired water and sediment samples to detect Pacific salmon in frontier habitats within a well-established salmon system of the Skeena River watershed, northwest British Columbia. Paired samples were collected during aerial surveys in 2023-2024 and analyzed using validated assays and rigorous quality controls. Across sites and species, environmental DNA in water provided consistent detection of contemporary salmon presence, particularly in known-occupancy systems with high spawning abundance. Sediment environmental DNA detections were more variable but occurred frequently at sites where water samples did not detect fish. In discordant cases, sediment more often detects salmon than water, indicating that sediment integrates biological signals over longer temporal windows and captures emerging or early-onset, low-density habitat use missed by water sampling. Together, environmental DNA in water and sediment provide complementary perspectives on salmon occupancy across dynamic, glacier-influenced flow conditions. Environmental DNA surveys revealed salmon presence in multiple tributaries lacking recent or ancestral observations, demonstrating the capacity of paired-media monitoring approaches to identify emerging or intermittently used habitats in remote northern watersheds. Paired water-sediment environmental DNA surveys provide a practical, scalable, and noninvasive framework for detecting salmon habitat use across changing northern river systems. By combining real-time indicators of presence with longer term signals of intermittent or past use, this approach improves habitat inventories, strengthens cumulative-effects assessments, and enhances early detection of emerging habitats. Integrating paired-media environmental DNA into Indigenous-led monitoring and governance frameworks can help restore critical information flows at a time of declining conventional monitoring capacity, supporting proactive stewardship and informed decision-making under accelerating climatic and industrial change.