Cumulative anthropogenic activities in coastal regions are a major threat to their marine biodiversity. The consideration of coastal marine areas as social-ecological systems (CMSESs) can be useful for marine biodiversity conservation. This integrative approach incorporates social information that can link anthropogenic activities to marine biodiversity, providing opportunities for improving conservation policies tailored to the specific reality of the CMSESs. Here, we assessed the beta and alpha diversity of the shallow littoral fish communities present in the Andalusian CMSESs and explored how they relate to socioeconomic and marine environmental variables. We used underwater visual surveys to estimate the fish abundance data needed to calculate the alpha and beta diversity of the fish species. We quantified the species and functional beta diversity using abundance-based data. We also quantified species richness index as indicators of species alpha diversity, and functional evenness as indicators of functional alpha diversity. We found that the association of marine environmental and socioeconomic variables with biodiversity varied with CMSES. Empirical inclusion of biodiversity in social-ecological systems research of marine and coastal areas can provide insights on human-nature dynamics. This can contribute to design more effective marine biodiversity conservation programs that consider both the socioeconomic and marine environmental characteristics of each CMSES.