A systematic investigation of PCB in coastal sediments of the Baltic Sea was initiated in 1996 by retrieving dated subsurface layers (1992–1994) from 88 sites in 19 sheltered archipelago areas, where laminated sediments were found to be common. PCBs7 (HELCOM's standard sum of 7 congeners, ≈1/6 of total PCB) was quantified, as well as the abundance and isotopic composition of nutrients (N, C), in order to trace effects of eutrophication and potential influences on the turnover of PCB. In most of the areas, the median of PCBs7/C was within 70 to 120 ng g−1 C. This is similar to recent values in regional offshore sediments, and thus consistent with a rapid exchange between coastal and open waters. Elevated PCBs7 levels up to around 1000 ng g−1 C were found within 50 km from Stockholm. Here, but not in other areas, PCBs7/C increased linearly with the degree of eutrophication. This was evident from the isotopic composition of sediment N and C, reflecting local eutrophication as well as its link to freshwater input. In contrast, concentrations or ratios of nutrients in sediments were poor indicators of eutrophication. Our results demonstrate that the Stockholm watershed still is a source of both PCB and excess nutrients to the Baltic Sea, but do not support any enrichment or dilution of PCBs7/C ratios caused by eutrophication.