This study conducted a comparative analysis of benthic macroinvertebrate communities in the Fosu and Benya lagoons in Ghana, based on the anthropogenic effect on the two lagoons. Salinity, oxygen, temperature, conductivity, turbidity and pH were measured, invertebrate richness and species densities were determined. The AZTI Marine Biotic Index (AMBI) and multivariate statistics were used to determine the different responses of fauna to pollution. The fauna were categorized into five ecological groups based on the degree of tolerance of the different species to pollution: disturbance-sensitive species; disturbance-indifferent species, disturbance-tolerant species, second-order opportunistic species; and first-order opportunistic species. The Fosu Lagoon supported more pollution tolerant species, whereas the Benya Lagoon had more species that were sensitive to organic enrichment under relatively unpolluted conditions. Chironomus sp., which is adapted to virtually anoxic conditions, was the most abundant in the Fosu Lagoon whereas Nemertea sp. was the most abundant in the Benya Lagoon. The numerical and relative abundance (%) of all 7 taxa in the Fosu Lagoon was 1,359 and 92.35%, respectively. The numerical and relative abundance (%) of all 34 taxa in the Benya Lagoon was 2,459 and 87.52%, respectively. Expectedly, the level of dissolved oxygen in the less saline Fosu Lagoon was higher than that in the more saline Benya Lagoon. The reduced photoperiod and photosynthetic activities of aquatic plants might account for this trend. There is a need to implement comprehensive monitoring and management initiatives for sustaining the ecological health of coastal lagoons in Ghana in order to support the many people that depend upon these ecosystems for their livelihood.