Understanding the complexity of social-ecological systems is fundamental for achieving sustainability. Historically, humans have benefited from the ecosystem services offered by nature at the same time that natural systems have increasingly changed because of anthropogenic activities. The lack of methods to unveil and understand such associations might hinder the integrated management of coastal marine areas. In our study, we applied a methodological framework used in terrestrial systems to identify and spatially locate the coastal marine social-ecological systems (CMSESs) on the southern Mediterranean Spanish coast. These CMSESs represent areas with similar human-nature associations that result from sharing similar socioeconomic and marine environmental characteristics. We applied several multivariate analyses to identify and characterize these CMSESs. We found the presence of twelve CMSESs that suggest a co-evolution of the social-ecological associations in these areas. Our results highlight the need for integrated coastal planning and management that consider the specific characteristics and conservation challenges of each CMSES. Our study provides evidence that a successful methodological framework to identify and characterize social-ecological systems can be applied in coastal areas and contribute to integrated management for the sustainability of these fragile systems.