The structure and ecophysiological characteristics of phytoplankton assemblages were studied for 10 months in two lagoons of different salinity (40 and 90) in the saltern of Sfax (Tunisia), in relation to environmental factors. These assemblages were largely dominated by diatoms and dinoflagellates, which accounted for >90% of total abundance. A principal components analysis clearly differentiated the observations made in the two lagoons, the dominant correlate being the salinity. Euryhaline species and particularly diatoms developed preferentially in the less saline lagoon, and were largely replaced by stenohaline species represented by dinoflagellates, which were dominant in the more saline lagoon. Calculation of the pigment diversity index and the species diversity index showed that the phytoplankton assemblages studied were permanently in a juvenile stage, as the species restructuring related to environmental constraints did not allow them to reach the climax stage at any given time in their development. Despite the heavy constraint imposed by the salinity, it is evident that other environmental factors, e.g. temperature, play a role in the regulation of the planktonic communities. Finally, the difference in the size distribution of the total microbial biomass, estimated by the assay of particulate proteins, showed that there was a significant change in the community structure and the planktonic trophic networks, in parallel with the increase in salinity.