We examined how interactions among the three dominant species of the Macoma balthica community in the St-Lawrence estuary influence net biogeochemical fluxes and the composition of the sedimentary bacterial community. We manipulated the biodiversity of the community via combinations of Macoma balthica, Mya arenaria, and Nereis virens in sediment microcosms containing sieved and homogenized tidal-flat sediment. Each combination was adjusted to similar total biovolumes and in situ animal densities. Compared to treatments with single species, which were also adjusted to similar biovolumes and densities, combinations of multiple species changed the fluxes of oxygen, phosphate, ammonium, and nitrate across the sediment-water interface and altered the composition of the microbial community beyond the level predicted by linear addition of the single species effects. Most combinations involved positive interactions that increased net fluxes. Although N. virens dominated system behavior, we also observed positive interactions between the two bivalves, and between N. virens and M. balthica. Weaker interactions, sometimes negative, were observed between N. virens and M. arenaria. Most effects could be directly linked to total oxic sediment volumes and burrow volumes generated by the different species. N. virens had the maximum species-specific burrow volume/biovolume ratio, and its presence maximally impacted fluxes. The principal interactions between species that affect net solute fluxes reflect space occupation, life habit (position, location), and irrigation of burrows. These factors interact with reactive substrate distributions and remineralization patterns to produce particular flux balances. Future studies should include the relationships of biodiversity to spatial scales over which the functional groups are distributed, the volumes actively occupied and irrigated, production rates of burrows, and the depths to which the organisms burrow.