Benthic invertebrates have important ecosystem engineering functions (bioturbation and biodeposition) in freshwater and marine benthic systems. Bioturbation and biodeposition affect the metabolism of the water–sediment interface through modification of water–sediment fluxes or organic-matter enrichment of sediments by biodeposits. The functional significance of these processes depends strongly on the type of invertebrate activities (the functional traits of the invertebrates) and on the modulation of this activity by environmental conditions. The aim of my article is to propose a common framework for the role of bioturbation/biodeposition in benthic habitats of both marine and freshwater environments. In these ecosystems, hydrological exchanges between the water and sediments (interstitial flow rates) control the microbial activity inside sediments. The ability of ecosystem engineers to influence benthic microbial processes differs strongly between diffusion-dominated (low interstitial flow rates) and advection-dominated (high interstitial flow rates) habitats. Bioturbation/biodeposition may play a role in diffusion-dominated habitats where invertebrates can significantly modify water and particle fluxes at the water–sediment interface, whereas a slight influence of ecosystem engineers is expected in advection-dominated habitats where fluxes are predominantly controlled by hydrological processes. A future challenge will be to test this general framework in marine and freshwater habitats by quantifying the interactions between the functional traits of species and the water–sediment exchanges.