Bioturbation activities of tubificid worms play a major role in nutrient cycling and microbial processes occurring at water–sediment interfaces of freshwater environments. Nevertheless, evidence of significant contributions of worms to ecosystem functioning largely arises from experiments performed at laboratory scales, because studies exploring the role of tubificid worms in the field are scarce. Therefore, this study aimed to test the influence of tubificid worms on benthic habitat structure and functioning in field experiments. According to literature, we predicted that feeding activities of tubificid worms would increase the percentage of clay and silt particles, the bacterial growth and microbial activities in the top sediment layer. The experiment was performed at the water–sediment interface of a shallow wetland. Enclosures with and without addition of the tubificid worm Limnodrilus hoffmeisteri were used to quantify the influences of tubificid worms on the sedimentary habitat (sediment grain size distribution, water‐filled porosity using microtomography), the biofilm (algal biomass, bacterial abundance, total organic carbon and total nitrogen, microbial enzymatic activity, photosynthetic activity and efficiency of the photosystem II) and the benthic fauna. Measures were performed before worm addition and at the end of the experiment. After 6 weeks, the proportion of fine sediment particles (<63 μm) and the water‐filled porosity were significantly modified by the bioturbation activities of tubificid worms. The bacterial abundance was stimulated by twofold, the microbial hydrolytic activity by +35% and the algal biomass by +40%. The field enclosures with and without L. hoffmeisteri showed differences in benthic invertebrate assemblages, especially for nematodes that were excluded from enclosures with worms. Our results indicate that bioturbation mechanisms and impacts reported from laboratory experiments with tubificid worms are not only significant at a field scale, but also highlight unpredicted interactions with other benthic organisms (autotrophic compartment of the biofilm and invertebrates).