Comparing lake surface water, deep-water, and sediment for fish environmental DNA detection as part of Indigenous-Community Based Monitoring in Alberta’s Oil Sands Regions

Environmental DNA (eDNA) is an increasingly valuable, non-invasive tool for monitoring freshwater fish biodiversity. While most eDNA studies rely on surface water sampling, few have compared the effectiveness of surface water, deep water, and sediment samples in lake ecosystems. This study evaluates these sampling approaches across five lakes in Alberta’s Oil Sands Region, an area of economic and cultural significance where Indigenous communities are leading monitoring through Indigenous Community-Based Monitoring programs. Using species-targeted quantitative PCR (qPCR) assays, we assessed fish detection effectiveness to inform long-term monitoring strategies. Deep-water samples consistently yielded the highest species detection rates and eDNA copy numbers across all lakes, outperforming both surface water and sediment. Surface water showed moderate detection success, while sediment exhibited variable performance, occasionally detecting benthic or rare taxa absent in water samples. These findings demonstrate the value of eDNA for documenting baseline fish communities and identifying rare or at-risk species. Yet, effective integration into ongoing monitoring programs requires tailoring survey designs to the ecological traits and behaviors of target species, including habitat preferences, life history strategies, and movement patterns. Based on this exploratory work, we recommend a multi-habitat, multi-season sampling framework aligned with fish ecology and lake dynamics to maximize detection accuracy and achieve a more comprehensive representation of aquatic biodiversity.