People living in coastal areas have the advantage of accessing a high level of ecosystem services, but are also exposed to the dangers inherent in living by the sea in an area prone to natural disasters. To achieve sustainable utilization of the high ecosystem services of coastal areas, establishment of an effective marine policy based on regional characteristics of human–nature interactions is essential. We compared the structure of perceived satisfaction for five components of human well-being (‘Security’, ‘Basic material for a good life’, ‘Good social relations’, ‘Health’, and ‘Freedom of choice and action’) derived from coastal ecosystem services among three sites in Japan (Wakasa, Sanriku, and Shima) that share the same natural and social backgrounds: highly dependent on fisheries industry, located in the same climate regime (temperate zone), and have similar topographical features (ria coast). Structural equation modeling using the results from questionnaire surveys showed that the three sites shared a common basic structure of the interactions among the five components of human well-being. However, the intensity of interactions among components differed among the three sites. Questionnaire surveys on anxiety about natural disasters and future access to marine ecosystem services were simultaneously conducted at the three sites. The site-specific anxieties were responsible for the difference in the interactions among the five components of human well-being. We propose a method that quantitatively evaluates both positive (satisfaction) and negative (anxiety) aspects of respondents’ subjective assessment as a useful tool for understanding the diversity of human–nature interactions caused by the region-specific natural and social backgrounds of coastal areas.