Benthic macrofaunal populations through their feeding, bioturbation, burrow construction and sediment irrigation activities have profound influences on organic matter inputs to marine sediments (biodeposition) and on the vertical distribution of deposited organic matter within the sediment. These effects in turn influence the rates and pathways of organic matter mineralisation, and element cycles. Similarly, bioturbation, burrow construction and burrow irrigation are major determinants of sediment-water column fluxes of oxygen and nutrients. In this review, I discuss the influences of the different benthic macrofaunal feeding (functional) groups on mineralisation processes and sediment-water column fluxes of particulate and dissolved nutrients. How these effects influence diagenic processes, the balance between aerobic and anaerobic processes, and the redox status of the surficial sediments. Finally, I discuss some of the limitations of the predominantly laboratory techniques which have been used to study “macrofaunal effects” and how this hinders the inclusion of the effects in quantitative sediment biogeochemical models.