We assessed the influence of benthic communities on sediment properties in large defaunation experiments in replicated 16 m2 plots on a tidal flat in the Westerschelde estuary (SW Netherlands). We compared microphytobenthos and benthic macrofauna recovery and recolonisation between control and defaunated sediments during 8 mo following the defaunation, focussing on how the temporal scale of biological responses interact with the temporal scale of sedimentological developments (grain size, bed level, erosion threshold). In the first month, microphytobenthos (surface chl a content) increased to >3 times the control values and remained elevated until 3 mo after the start of the experiment. Macrofaunal recovery started with mobile mudsnails after only a few days. Tube-building macrofauna dominated first, followed by surface-disrupting species. Both groups became much more dominant in defaunated than in control plots. Surface pelletisers almost recovered to control levels after 4 mo, while biodiffusing bivalves did not recover during the course of the experiment. Mud content of the sediment surface first increased with chl a, but started to decrease, concomitant with an over-representation of surface disruptors. A similar trend was observed for critical erosion threshold. Bed elevation of experimental plots exceeded controls by several cm after 1 mo, and remained higher through summer. The time scales of changes in microphytobenthos and in abiotic characteristics of the sediment were largely set by the time scale of macrofauna recovery. Macrobenthos plays a critical, but complex role in the dynamics of intertidal sediments.