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Global freshwater biodiversity is declining at rates greater than in terrestrial or marine environments, largely due to habitat alteration and loss. Pacific salmon are declining throughout much of their southern range due to a combination of pressures in their marine and freshwater habitats. There is, therefore, an urgent need to understand the main drivers of decline to inform both fisheries and land-use management. Here, we draw on a suite of freshwater habitat pressure indicators to test whether we can detect relationships between them and trends in Pacific salmon spawner abundance throughout British Columbia. We related trends in spawner abundance (n = 3691 populations) to ten habitat pressure indicators that represent a snapshot in time of the level of degradation in salmon freshwater spawning habitats (e.g., Equivalent Clearcut Area, percent watershed area impacted by urban development or agriculture).Evidence of relationships between freshwater habitat pressure indicators and trends in spawner abundance was weak at the province-wide scale, while variable in both direction and magnitude at the watershed scale likely due to the mediating effects of regional biological and physical factors. We used these empirical relationships to assess the vulnerability of individual species and regions to increasing habitat pressures. Vulnerability was highest when multiple conditions coincided: when salmon were sensitive to the habitat pressure indicator, the current level of disturbance under that indicator was moderate or low, and populations were declining but not yet at rates high enough to be deemed “threatened”. These findings highlight the need to consider the current state of the landscape and of populations when assessing where habitat protection might have the greatest benefit for biodiversity conservation. Strategic recovery planning for Pacific salmon requires multi-scale approaches that account for the diversity and complexity of relationships between habitat disturbance and population dynamics.