To assess the effect of variability in hydrodynamic stress on benthic assemblages we investigated whether deposit-feeding macrobenthos performs a unimodal response to an intertidal flat hydrodynamic stress gradient, congruent with the intermediate disturbance hypothesis (IDH), and whether this response is related to assemblage-wide biological trait displacements, reflecting species sorting mechanisms. Patterns in diversity and assemblage-wide biological traits were explained to a large extent by hydrodynamic stress and reflected in a significantly differing assemblage structure between stress levels. Our data did not support the IDH, since species richness and diversity peaked at low stress, whereas evenness was lowest at intermediate stress, suggesting that species sorting in response to hydrodynamic stress, rather than competitive exclusion at low stress, drives the diversity stress response. The decrease in species richness and diversity towards the hydrodynamically harsher low intertidal was reflected in the assemblage-wide shifts towards a lower dietary dependency on microalgal carbon and a deeper living position. Intermediate stressed assemblages were associated with a shift towards a more resistant development mode to superficial sediment disturbance. This is suggested to result from species sorting in response to Cerastoderma edule interference from bioturbation, which peaked at intermediate hydrodynamic stress where optimal hydrodynamic conditions for suspension feeders prevail. The present study demonstrated that the alteration of the natural hydrodynamic regime will significantly affect tidal flat benthic community composition and, hence, ecosystem functioning. Additionally, our findings reveal that inhibitory biophysical interactions, such as interference from bioturbation, should be incorporated in environmental stress biodiversity models.