Coastal and estuarine environments are particularly productive ecological systems and can provide protein and nutrient exports to adjacent marine ecosystems. In spite of this, studies of fish school migration patterns between lagoons and the sea are lacking. In 1999, fish samplings combining fishing and acoustic sonar field data collection were performed in two shallow water channel lagoons to monitor fish school diel migration (lagoon-sea). Lagoon fish assemblages included 15 species and 10 families. The estimated abundances and the fishes' swimming characteristics permit those detected by sonar to be selected according to 3 criteria. Direct sampling by cast net confirmed that Dicentrarchus labrax schools were present during the autumn migration period. In situ horizontal sonar observation in shallow water bodies constitutes a powerful tool for the Study of fish behaviour. Fish school migration within the range of values recorded was not affected by current velocity (maximum 0.83 m/s). No relationships among school shape, surface area or migratory direction were found. The amphidromous schools were small (0.3 to 15 in 2) and observed mainly at night. Migratory behaviour appeared to be determined to some extent by fluctuations in lagoon salinity and temperature. Consistent with the 'multi-transit' hypothesis, which states that schools pass several times in front of the sonar transducer before moving toward or away from the lagoon, the net flow of fish was less than that predicted by the sonar methodology. Thus the multi-transit behaviour hypothesis should be considered when interpreting fish Population transfer data gathered with acoustic methods using a single transducer in rivers, estuaries, or channels. In addition, the exclusive use of echosounder Could generate major biomass underestimation when the fish are grouped in schools. (c) 2006 Elsevier B.V. All rights reserved.