In coastal environments, strong feedback can exist between benthic fauna and sediment dynamics. Benthic populations can modify sediment dynamics through biofiltration and bioturbation, while hydro- and sediment dynamics directly determine local environmental conditions for benthic organisms. However, these complex feedbacks are difficult to study in situ. Here, we carried out mesocosm experiments to characterize the effects of a benthic species (the gastropod Crepidula fornicata) on mud dynamics under hydrodynamic conditions representative of their natural habitat. Different experimental tests related to the inclusion (or not) of dead or live crepidula reveal that biofiltration can increase particle settling up to 40%. Flocculation, which is strengthened by organic matter enrichment in shell beds, also substantially increases particle settling. Thus, both processes enhance sedimentation above live crepidula habitats. Furthermore, these experiments highlight serious technical, physical and biological challenges that have to be tackled for properly investigating bio-physical interactions.