Chile has established unique marine resource user rights to reduce resource over-exploitation and expand economic opportunities in coastal areas. These rights sometimes overlap, so that one household might be involved in more than one activity, and also leave out some people who might want to participate. To help decision-makers develop policies aimed at increasing incomes through small-scale aquaculture (SSA), we collected and analyzed data to identify the factors determining households’ choices of activities, as well as the factors determining income levels, in the Los Lagos region of southern Chile. We found that the influence of the local biogeographic setting on activity choices and indirectly on incomes, paired with a general unwillingness to move to places where large incomes were possible, implies the need to target different aquaculture policies in different locations within the region. We also identify locations, activities, and seasons in which there is currently not enough work available, which suggests opportunities for households to diversify their marine resource activities.