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Expected higher intensity and frequency of extreme climatic events is likely to affect considerably coastal shallow areas. We studied the impact of a windstorm event (WSE) on relevant biogeochemical characteristics in the water column and intertidal sediments of the inner Cadiz Bay (Spain), as a model for shallow coastal environments. Samples were collected before, during and after a WSE in two sites with different sediment characteristics, sandy and muddy, located in opposed sides of the inner bay to cover maximum variability. Total suspended solids (TSS), chlorophyll a (Chla) and most dissolved inorganic nutrients increased transiently in the water column during WSE, showing an evident transfer of matter from the sediment. TSS and Chla in water column were linearly related among them and with wind speed, while concentration of inorganic nutrients was not. This difference suggests that the concentrations of inorganic nutrients in the water column were not the direct result of the release during resuspension, but that further biogeochemical processing occurs in the water column. TSS and Chla estimated by Sentinel-2 imagery confirmed the impact on the water column, but also a considerable degree of spatial heterogeneity. WSE affected sediment O 2 vertical distribution, net metabolism, Chla, organic carbon, total nitrogen and pore water NH 4 + and PO 4 3- in different degree depending on sediment characteristics and hydrodynamics conditions. Overall, these changes were transitory, returning the system very soon to pre-WSE conditions. Clearly WSE increased benthic-pelagic coupling in shallow coastal areas, increasing resuspension and exchange of nutrients between the sediment and the water column. During WSE, the outwelling from these shallow environments can increase considerably, likely affecting coastal productivity.