eDNA provides accurate and precise estimates of abundance by integrating bioenergetics and particle mass-balance

Anthropogenic activities have led to an unprecedented crisis in freshwater biodiversity loss. The capacity to monitor the abundance of wild populations is critical to conserving biodiversity, but conventional physical specimen collection methods are invasive, costly, and labour-intensive. Environmental DNA (eDNA) offers a promising alternative, being easy to sample, with studies under controlled laboratory conditions showing consistent correlations between eDNA concentration and abundance. However, applying eDNA to monitor abundance remains contentious, as eDNA particle dynamics and the ecology of eDNA production can decouple this relationship in natural ecosystems. To address this, we integrated bioenergetics and mass-balance frameworks to relate eDNA concentrations to freshwater fish population abundance estimated through conventional mark-recapture in Brook Trout ( Salvelinus fontinalis ) across nine Rocky Mountains lakes, five of which underwent size-selectively harvest over two years. Our integrated framework improved the variance explained in eDNA concentrations from 24% to 71%. The integrated model accurately distinguished most abundance estimates across populations and sampling periods, detecting both natural and harvest-induced reductions in abundance within several populations. This study is the first to empirically integrate the DNA production ecology and particle dynamics, demonstrating that properly accounting for ‘the ecology of eDNA’ enables rapid, accurate abundance quantification. We also discuss future research and applications of eDNA in light of these results.