Environmental DNA facilitates accurate, inexpensive, and multi‐year population estimates of millions of anadromous fish

Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. However, the efficacy of environmental‐DNA‐based indices of abundance for long‐term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark‐recapture population estimates for eulachon (Thaleichthys pacificus) and ‘eDNA rates,’ which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark‐recapture population estimate, explaining 84.96% and 92.53% of the deviance respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a > 80% cost savings over mark‐recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark‐recapture is infeasible.