Environmental DNA Reflects Differences in Freshwater Habitat Use Between Two Pacific Salmonids at Fine Temporal Scales

ABSTRACT Environmental DNA (eDNA) has emerged as a powerful tool to detect aquatic species, providing a non‐invasive survey option for applications in freshwater fisheries, including delineating habitat use and informing stock management strategies. For species like salmonids with life stage‐specific habitat requirements and timing, effective use of eDNA for species detection at fine spatial and temporal scales is contingent upon a robust understanding of eDNA detectability across all life stages. We conducted a 12‐month eDNA survey in two Canadian rivers to describe temporal variation in eDNA concentrations of two anadromous fishes, Chinook ( Oncorhynchus tshawytscha ; Salmonidae) and coho salmon ( O. kisutch ), and relate this to important life history periods including spawning, egg incubation, fry emergence, rearing, and outmigration. We sampled downstream of known spawning grounds and found discharge‐corrected eDNA concentrations were closely associated with known migratory patterns across species. For example, eDNA concentrations peaked during fall spawning for both species and followed similar monthly trends in summer. Sharp declines in eDNA were observed following spawning and concentrations remained low until spring when small spikes were detected as a result of fry emergence and rearing. We also found evidence of eDNA concentrations providing species detection at fine temporal scales in rivers, as a large hatchery release of Chinook was detected by eDNA only on the day of release and not on subsequent days. These results demonstrate eDNA as a temporally specific and effective detection tool across salmonid freshwater life stages and highlight the promise of eDNA for assessing major life history periods of Pacific salmon in freshwater. Overall, our work builds on the rapidly growing field of eDNA for applications to fish and fisheries and reinforces the promise of this technology for improving current management practices.