Intertidal estuaries are becoming increasingly eutrophicated due to anthropogenic stressors, with bivalve restoration offering promise for the remediation of eutrophication. Manipulating the density of large infaunal bivalves provides sediment stability, microhabitats for epibionts, and enhances solute exchanges and nutrient transformation in estuaries. The ubiquitous suspension-feeding cockle, Austrovenus stutchburyi, provides great potential for shellfish restoration in New Zealand estuaries. We studied the influence of Austrovenus restoration in a eutrophicated estuary (Jacob’s River Estuary, Southland) by manipulating the biomass of natural populations of Austrovenus and measuring ecosystem functions (carbon and nitrogen cycling) and functional traits of associated macrofauna across gradients of mud content. Increasing Austrovenus biomass altered the community composition of benthic infauna by decreasing the abundance of soft-bodied deposit-feeders. Increasing Austrovenus biomass elevated surface (0 – 2 cm) and sub-surface (5 – 10 cm) porewater ammonium (NH4+) concentrations. High NH4+ concentrations correlated with higher decay rates of organic carbon on the sediment surface, but the effect was context dependent with mud content important. These findings suggest that increasing Austrovenus biomass alters the infaunal community and alters carbon and nitrogen cycling in estuarine sediments but highlights the importance of considering background stressors like mud inputs for enhancing ecosystem functions with shellfish restoration.