Fishermen have long observed the sudden change of shoaling behaviour of small pelagic fish following a strong wind event. The phenomenon was thereafter confirmed by fisheries scientists using acoustic tools. In this study, we report our observations made with acoustics to measure disorganization of the previously observed spatial distribution and shape of shoals that occurred after a wind event. The measurements were made during a fisheries research cruise in the Bay of Biscay (NE Atlantic) aimed at determining i) small pelagic fish species abundance and ii) the individual nutritional state of anchovies (Engraulis encrasicolus L.) via evaluation of their RNA/DNA ratio. A spatial fine-scale study was conducted in two of the main breeding areas for anchovy, one located near the plume of a large river (haline stratification) and the other in an open sea location over the continental shelf break (thermal stratification). After a strong wind event, a change of the spatial and bathymetric distribution of the fish community, including anchovy, was observed in the open sea area, whereas no effect was detected in the near shore area. The RNA/DNA ratios determined in anchovy white muscles were quite similar in both areas before the wind event. Afterwards, they remained unchanged near the shore but were significantly reduced in the open sea location. This difference can be explained by the disparity in the strength of the stratification (i.e. haline versus thermal), but a change in the species composition of the fish community may also have played a role.