The main objective of this study was to measure the impact of benthic invertebrate diversity on processes occurring at the water–sediment interface. We analyzed the effects of interactions between three shallow water species (Cerastoderma edule, Corophium volutator, and Nereis diversicolor). The impacts of different species richness treatments were measured on sediment reworking, bacterial characteristics, and biogeochemical processes (bromide fluxes, O2 uptake, nutrient fluxes, and porewater chemistry) in sediment cores. The results showed that the three species exhibited different bioturbation activities in the experimental system: C. edule acted as a biodiffusor, mixing particles in the top 2 cm of the sediments; C. volutator produced and irrigated U-shaped tubes in the top 2 cm of the sediments; and N. diversicolor produced and irrigated burrow galleries in the whole sediment cores. C. edule had minor effects on biogeochemical processes, whereas the other species, through their irrigation of the burrows, increased the solute exchange between the water column and the sediment two-fold. These impacts on sediment structure and solute transport increased the O2 consumption and the release of nutrients from sediments. As N. diversicolor burrowed deeper in the sediment than C. volutator, it irrigated a greater volume of sediments, with great impact on the sediment cores. Most treatments with a mixture of species indicated that observed values were often lower than predicted values from the addition of the individual effects of each species, demonstrating a negative interaction among species. This type of negative interaction measured between species on ecosystem processes certainly resulted from an overlap of bioturbation activities among the three species which lived and foraged in the same habitat (water–sediment interface). All treatments with N. diversicolor (in isolation and in mixture) produced similar effect on sediment reworking, water fluxes, nutrient releases, porewater chemistry, and bacterial characteristics. Whichever species associated with N. diversicolor, the bioturbation activities of the worm hid the effect of the other species. The results suggest that, in the presence of several species that use and modify the same sediment space, impact of invertebrates on ecosystem processes was essentially due to the most efficient bioturbator of the community (N. diversicolor). In consequence, the functional traits (mode of bioturbation, depth of burrowing, feeding behaviour) of an individual species in a community could be more important than species richness for some ecosystem processes.