The relationships between nutrient dynamics, microbial community, and macrofauna are important in bioremediation systems. In this study, we examined the effects of marine clam Scapharca subcrenata sedimentary activities on the microbial assemblages, benthic nutrient chemistry, and its subsequent remediation impacts on organic effluent in the sediment of an aquaculture wastewater bioremediation system. The results showed that microbial community composition differed significantly in the clam area (ANOSIM, R = 0.707, P = 0.037). Pyrosequencing of bacterial 16S rRNA gene revealed a total of 48 unique phyla, 79 classes, 107 orders, 197 families, and 321 genera amongst all samples. The most dominant bacterial assemblages were Proteobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, and Actinobacteria, with Bacteroidetes and Firmicutes significantly higher in all treatment samples than control ( P < 0.001). All dominant phyla in the list were shared across all samples and accounted for 89% (control) and 97% (treatment) of the total 16S rRNA. The nutrient flux rates from the sediments into the water (treatment group) were 51% (ammonium), 88% (nitrate), 77% (nitrite) and 45% (phosphate) higher, relative to the control implying increased mineralization, degradability, and mobility of the benthic nutrients. Similarly, significantly increased oxygen consumption rates were evident in the clam area signifying improved oxygen distribution within the sediment. The organic effluent contents associated with total- organic matter, carbon, nitrogen, and, phosphate were lower among the clam treatments relative to the control. Our results describe the potential roles and mechanisms contributed by marine bivalve S. subcrenata on benthic-bacterial-community assembly, nutrient balance, and effluent reduction in the sediments of aquaculture wastewaters bioremediation system.