The Archipelago Sea in the northern Baltic has been subjected to large-scale cultural, economic and ecological changes, especially during the last three decades. Environmental threats originate from both basin-wide sources, affecting the whole Baltic Sea, and from local sources, such as nutrient loading from nearby river outflows, intense agriculture, fish farming, ships' traffic, boating, and man's physical impacts on the landscape and seascape. Both the Aland archipelago and the Archipelago Sea have been listed as hot-spots by HELCOM, Baltic Marine Environment Protection Commission, eutrophication being the main threat to the aquatic environment. In this study we review how biological communities have reacted to an increase in man-induced multisource stresses. Changes in plankton, benthic animals, macroalgal assemblages and fish communities have been documented in most parts of the Baltic Sea since the 1970s. What remains to be understood is the importance of these structural changes for the functioning of the Archipelago Sea ecosystem under various levels of human impact.