We demonstrate how watershed-scale aquatic ecological risk assessments (ERAs) for multiple Stressors are conducted. Most ERAs focus on toxic chemicals, however, many Stressors may affect aquatic ecosystems within watersheds. Other watershed-scale aquatic Stressors include physical and hydrologic Stressors, and physical habitat degradation. We demonstrate a method for quantifying the risks of these other Stressors and comparing the resultant non-toxic chemical risks with toxic chemical risks, using habitat models to estimate the effects of non-toxic chemicals on habitat quality. This information is then compared to the risks from chemical toxicity, and the results used to compare the relative risks of chemical toxicity with the risks of other types of Stressors, to identify the most limiting factors. With this information, the most beneficial types of ecological restoration can be identified and resources allocated to provide the greatest ecological benefit to the watershed.