Understanding the mechanisms that drive complementary interactions among species is key to the progress of the debate over the role of biodiversity in ecosystem functioning. In addition, interspecific interactions among physical ecosystem engineers have rarely been framed in the context of biodiversity experiments. Here, we provide an empirical test of how the physical niche space of species influences the effects of the biodiversity of bioturbators on cross-habitat nutrient fluxes in benthic sediments. In the laboratory, we orthogonally manipulated the number and composition of three benthic invertebrate bioturbator species that differ in the dimensions of their bioturbating space niche; i.e. their vertical distribution in the sediment over a gradient of sediment depth and volume. The ammonium (NH4-N) flux from the sediment to the water was positively related to bioturbator species richness only in the sediments with the deepest depth and greatest volume. The non-additive effects of bioturbator species richness on the benthic–pelagic NH4-N flux increased linearly with sediment depth and volume, but only in the three-species mixtures. Furthermore, no individual species dominated the rates of H4-N fluxes, indicating that biodiversity effects were mainly driven by complementarity. These results suggest that sediment bioturbating space mediates the magnitude of non-additive effects among the three invertebrate species and sheds light on the importance of physical niche space in modulating the positive effects of biodiversity on ecosystem functioning.