Long-term changes in sediment macrofauna communities at two sites affected by fish farming in the Archipelago Sea, south-west Finland have been investigated. Sampling stations in the Särkänsalmi Strait and Kaukolanlahti Bay, previously investigated 1982-1991, were revisited in 1994, 1995 and 1998 to detect signs of recovery following a decrease in organic load since 1990 and 1991, respectively. The results indicate a partial recovery in Särkänsalmi during post-pollution years, whereas no improvement has taken place in Kaukolanlahti. The improvement in Särkänsalmi is shown by a significant increase in the number of species and total abundance, and by the community structures becoming more similar over time. On the other hand, a significantly decreased number of species, abundance and biomass values over time as well as the occurrence of defaunated anoxic sediments, are clear signs of continued deterioration in Kaukolanlahti. Differences in the recovery potential of the two water areas are interpreted as consequences of topography and water exchange patterns causing differences in oxygen saturation.