This article focuses on the ecological role of benthic macrofauna on nutrient dynamics and benthic-pelagic coupling in the Baltic Sea with relation to eutrophication. Generally, benthic macrofaunal activities have large effects on sediment biogeochemistry and often with stimulatory effects on processes that counteract eutrophication, i.e., denitrification and increased phosphorus retention of the sediment. The degree of faunal impact on such processes varies depending on faunal density and functional group composition. The effect of macrofaunal activities on sediment nutrient dynamics can also result in a higher nitrogen: phosporus ratio of the sediments efflux compared with sediments without macrofauna. Increased internal nutrient loading during eutrophication-induced anoxia is suggested to be caused both by altered sediment biogeochemical processes and through reduced or lost bioturbating macrofauna and thereby a reduced stimulatory effect from their activities on natural purification processes of the Baltic Sea ecosystem.