Inter-annual variation in the composition of the soft bottom macrobenthic communities of two undisturbed lagoons, in Amvrakikos Gulf, Ionian Sea, Greece, was investigated over three consecutive summers. The environmental parameters that showed the greatest variability were organic carbon of the sediment and salinity. The species found were typical of lagoonal systems, the most common and abundant of which were Abra ovata, Mytilaster minimus and, in the most enclosed areas, larvae of chironomids. Multivariate analysis registered community changes, which were mostly caused by changes in species dominance. Structural community characteristics such as number of species, number of individuals and diversity did not show significant differences among years except in the stations with least water exchange with the sea.