Sediment cores were collected from April to August 2004 on tidal mudflats of the macrotidal Marennes-Oléron Bay (SW France), famous for the cultivation of Pacific oysters (Crassostrea gigas). The response of living (stained) benthic foraminifera to short-term biogeochemical disturbances in the sediment and overlying water, which may be involved in oyster summer mortality, was monitored. Short-term hypoxia occurred in early June, in conjunction with a sudden rise in temperature. In mid-June, the ammonia content of sediment porewater increased, leading to potentially maximal flux towards overlying waters. Foraminiferal assemblages, particularly in the topmost layer, were altered. Ammonia tepida was the most tolerant to temperature increase and hypoxic conditions whereas Brizalina variabilis and Haynesina germanica were sensitive to organic degradation and hypoxia. Cribroelphidium gunteri was the most opportunistic during recolonisation. Benthic foraminifera showed that short-term biochemical changes in the sediment are toxic and may be involved in the summer mortality of Pacific oysters.