Biodiversity and complex ecosystems within marine protected areas (MPAs) are often threatened by human activity and the multiple impacts it can have on the environment. A relative risk model was developed as a decision-making tool to help managers of MPAs focus their conservation and protection efforts. Using this tool, it is possible to map the areas most at risk, identify the human stressors involved, and test management strategies that could reduce risk and increase the overall level of environmental protection. A user-friendly computer interface was developed to facilitate its use by scientific teams and managers. The application of the relative risk model to the Saguenay-St. Lawrence Marine Park (SSLMP) allowed the mapping of the zones most at risk during the summer, when human activity is most intense and the stressors are most numerous. Results show that the areas most at risk in the SSLMP are the mouth of the Saguenay Fjord and the coastal zone near Les Bergeronnes. The model allows simulations (e.g., increasing or decreasing one or more stressors) and estimates the relative effectiveness of given conservation actions.