Abstract. – Two Tunisian lagoons and a coast location, diversely subject to anthropogenic activities and differing according to their degree of communication with the sea, were studied seasonally. The principal environmental variables (temperature, salinity and dissolved oxygen) were measured in situ. Jointly, main benthic macrofauna factors and the AZTI Marine Biotic Index (AMBI) were determined and analyzed. Results show that the seasonal fluctuations of the benthic communities structure differ in the three studied sites and are controlled mainly by the pollution and the hydrodynamic flow. In the first almost enclosed area (southern lagoon of Tunis) where measured environmental factors are more fluctuating and anthropogenic activities are important, the benthic community is more affected all year. The total abundance varies from 1279 to 7547 ind./m² and the specific richness from 31 to 61 species, however the evenness does not exceed 0.25 all year. In the other almost enclosed area (lagoon of Ghar El-Melh) which is less exposed to anthropogenic activities, fauna synthetic factors are less fluctuating, the abundance varies from 362 to 959 ind./m², the specific richness from 29 to 52 species and the evenness from 0.33 to 0.61. Also, in this site, first signs of degradation appear only in autumn in most stagnant waters. However, in the bay of Tunis and despite the strong anthropogenic pressures, the benthic community seems to be in satisfactory environmental conditions due, certainly, to the stronger hydrodynamic flow. In this coastal area, fauna synthetic factors are clearly less fluctuating between the two studied seasons, winter and summer. They are respectively 236-799 ind./m² for the abundance, 50-54 species for the specific richness and 0.43-0.73 for the evenness.