Brook trout (uinipeku-matemeku, Salvelinus fontinalis) and Atlantic salmon (ushashameku, Salmo salar) are both emblematic species of the province of Quebec for their popularity with recreational, commercial, and Indigenous food, ceremonial, and social fisheries. Both species are also currently experiencing population declines throughout most of their range, likely due to habitat fragmentation, competition for resources (i.e., food or habitat), fishing pressure, and climate change. Anticosti Island, a recently named a UNESCO World Heritage Site, is a well known destination for brook trout and Atlantic salmon fishing with populations of various health statuses. We propose an integrative model to identify the links between the environment and the various mechanisms underlying the ecophysiology and habitat preferences of Anticosti Island salmonids using otolith and water trace metal signatures, river morphology, and biodiversity metrics through environmental DNA. In August 2024, 8 rivers on Anticosti island were sampled for environmental DNA, water chemistry, and examined for river morphological characteristics. This data collection and model development will be useful for future ecosystem restoration plans and conservation goals for Brook trout and Atlantic salmon populations throughout the province of Quebec.