The variations of acetylcholinesterase activity, considered to be a biochemical biomarker of organophosphorus and carbamate compounds, was followed in Mediterranean clams (Ruditapes decussatus) and mussels (Mytilus galloprovincialis) as a function of season and sampling sites in the lagoon of Bizerta (Tunisia). Results show that acetylcholinesterase activity in clams collected from station A was the lowest and was so throughout the year. This low activity may be due to the input of non-treated waste waters in the lagoon. Heavy metal contamination has been reported in the sediments of this area, suggesting that acetylcholinesterase activity in clams may be inhibited by this type of pollution. Clams harvested from station F, a site adjacent to an agricultural area, were characterized by a decrease in acetylcholinesterase activity, especially after rain periods. Clams from station J presented the highest activity throughout the greater part of the year. This phenomenon may imply that this location is less affected by pollutants inhibiting AChE activity than the others. In the mussels from station C, located in the channel from the lagoon to the Mediterranean and submitted to pollutants (urban wastes from Bizerta and hydrocarbons from the maritime traffic), acetylcholinesterase activities were lower than in those from station J. In conclusion, the variations in acetylcholinesterase activity observed between stations in both species may be the result of pollution and of the environmental conditions.