ABSTRACT: Current and projected rates of extinction provide impetus to investigate the consequences of biodiversity loss for ecosystem processes. Yet our understanding of present day biodiversity–ecosystem functioning relations contrasts markedly with our understanding of the responses of species to changes that have occurred in the geological record. Of the experiments that have explicitly tested the relationship between biodiversity and ecosystem functioning, few have attempted to reconcile whether the underlying process that gives rise to the observed response is affected by biodiversity in the same way as the observed response. In the present study, we use benthic macrofaunal invertebrates to examine and distinguish the effects of species richness and species identity on bioturbation intensity, a key mechanism that has been important on evolutionary timescales regulating ecosystem functioning in the marine benthos. Our study identifies significant effects of species richness that reflect species-specific impacts on particle reworking that, in turn, lead to elevated levels of nutrient generation. However, our findings also suggest that the consideration of only bioturbation intensity forms an incomplete evaluation of bioturbation effects because the way in which species interact with the benthic environment does not necessarily reflect organism traits only associated with particle transport. Our study emphasises the need for caution when extrapolating from assumed knowledge of organism traits to how changes in species composition associated with ecological crises may impact ecosystem function. Nonetheless, the empirically derived mechanistic effects of bioturbation on ecosystem functioning documented here are sufficiently general to seek correlations between diversity and function in natural systems, including those from the palaeoecological record.