The biogeological organization of Thau lagoon was investigated through the granulometric analysis of surficial sediments and study of the qualitative and the quantitative distribution of benthic macrofauna and meiofauna. These show clearly that the lagoonal system is organized according to confinement as conceived by Guelorget and Perthuisot (1983 a; 1992), which depends upon the rate of exchanges with the open sea and the hydrodynamic pattern of the basin. The latter appears to be composed of a pair of lagoonal subsystems separated by a hydrodynamically unstable barrier. The northern subsystem displays the classical concentric organization of Mediterranean lagoons with a clearly defined hydraulic umbilicus. The southern subsystem displays a transverse original organization due to a large zone of exchanges with the sea through the sand bar. The basin is globally subject to only slight confinement, but displays signs of organic matter accumulation due to the intensification of shellfish culture.