Short-term changes in zooplankton community structure and distribution in relation to changes in hydrological features were studied during summer in two distinct areas of Arcachon Bay (France) from July to September 1986. One sampling site was chosen in the northern part of the bay, influenced by oceanic inputs, and the other one in the south-eastern part of the bay, close to an estuarine zone, influenced by the River Leyre's inputs. Three different zooplankton assemblages were identified according to a temperature–salinity gradient: (i) an estuarine assemblage dominated by Acartia bifilosa and Acartia tonsa; (ii) an autochthonous assemblage composed of Acartia discaudata; and (iii) a coastal neritic one composed of Paracalanus parvus, Oncaea venusta and Penilia avirostris. All these latter assemblages remained stable during most part of the study period. However, a brief climatic event (storm event) occurred in mid-August and gave rise to a sharp decrease in temperatures along with significant changes in zooplankton structure and distributions in the bay. The estuarine community vanished and was replaced by the autochthonous community. In the northern part of the bay, the coastal neritic community succeeded the previously observed autochthonous community. The effect of this brief climatic event was durable since recovery time lasted two weeks with regard to hydrological features and zooplankton communities. In addition, the climatic event also had ecological consequences since it permitted spreading of planktonic organisms from small-localized areas throughout the bay.