Rural, natural resource dependent communities are especially vulnerable to climate change, and their input is critical in developing solutions, but the study of risk perception within and among vulnerable communities remains underdeveloped. Our multi-disciplinary research team used a mixed-methods approach to document, analyze, and conceptualize the interacting factors that shape vulnerability and to explore community members' perceptions of the role and relative importance of climate change compared to other factors in three rural communities in Ecuador. Economic instability, lack of access to basic services, and environmental degradation are perceived as greater threats to community well being than increasing seasonal variability and flooding. Programs and policies directed at climate change adaptation should integrate climate and non-climate related stressors. Our findings also point to a greater need for collaboration across public health, poverty alleviation, and environmental management fields through practical research targeting assistance to vulnerable populations.