Human activities have impacted the coastal area of Antofagasta Bay for decades, particularly miners’ activities (loading of mineral concentrates of Cu, Zn, Pb, and Mg), port operations, tourism, desalination plants, artisanal fishing, and sewage discharge. Subtidal coastal benthic communities were assessed in 7 sectors with different magnitudes of anthropogenic disturbances between the years 2008 to 2011 at Antofagasta Bay. Transennella pannosa, Incatella cingulata, Crassilabrum crassilabrum, and Leukoma thaca dominated the communities in all years of study. Based on the type of feeding behavior, the highest biomass was evidenced for the suspensivore group in all years of study, followed by the carnivore species. The highest average richness and average Shannon diversity were observed in sectors with medium and high levels of disturbances. In contrast, the highest average species dominance was registered in a sector with low disturbances. Community structure differed significantly between the seven sectors over the four years. The analysis of classification and ordination showed the conformation of three groups of sectors based on their dissimilarities. The differences were best explained by the sectors with low and high disturbances and by the presence of bivalves, ascidians, gastropods, and algae. It was demonstrated that the reduction or absence of fishing pressure could explain species’ high richness and diversity. Likewise, the sectors under low disturbance pressure showed the highest biomass and dominance of species. The information obtained in the current work could be used to design management strategies for conservation, monitoring, and restoration programs.