Sediment run-off from land has been recognised as a threat to the biodiversity of shallow estuarine and coastal areas. Extreme rainfall events can cause flooding and landslides, which may result in rapid deposition of fine terrigenous sediments and have serious impacts on benthic communities. We designed a field experiment to study the response of intertidal benthos to such depositions of terrigenous clay. The experiment was conducted at 2 contrasting intertidal sites: a sheltered muddy sand habitat and an exposed sand habitat influenced by wind waves. Terrigenous clay (50% water content) was deposited in replicated experimental plots (2 m diameter) at each site in layers 0, 3, 6 or 9 cm thick. The initial response of the resident macrofauna and subsequent recolonisation was monitored over a period of 408 d. Physical and chemical properties of the experimental plots and wave climate at each site were also measured. The experiment demonstrated highly deleterious effects of catastrophic terrigenous clay deposition on estuarine macrobenthic communities. At both sites following clay deposition, the numbers of individuals were reduced by more than 50% after 3 d and by more than 90% after 10 d, irrespective of clay thickness. Mud crabs Helice crassa were the only animals able to emerge through the clay layer. They also exhibited elevated densities in clay treatments over the course of the experiment. After 28 d, a storm occurred (maximum wave height 0.4 m, period = 6 s) which dispersed the clay deposits at the exposed sandy site. Recolonisation of the surficial sediments was rapid at the exposed site following this wind-wave disturbance. However, deeper-dwelling animals such as large bivalves had not recovered to levels observed in the control plots by the end of the experiment. At the more sheltered muddy sand site, the clay deposition resulted in long-lasting habitat change; Although the clay was gradually broken up and re-colonised by small crabs and surface dwelling macrofauna, recovery was still incomplete 408 d after deposition. The results emphasise the role of wind-wave disturbance and transport of sediments and macrofauna with bedload, and the importance of bioturbation by crabs as facilitators of macrobenthic recovery after disturbance.