<p>The effects of environmental changes on contaminant fate in the ecosystem are poorly understood, even in the otherwise well-studied Baltic Sea. This area is considered one of the most polluted in the world and is currently undergoing rapid shifts related to climate change and eutrophication. In this study, we focus on the effects of an altered productivity base and changes in food web structure on contaminant concentrations in the commercially important Baltic herring, which is also a key-species in the ecosystem. In herring of known size and age, collected within the Swedish National Monitoring Program for Contaminants in Marine Biota during the past two to three decades, retrospective analyses of contaminant concentrations and stable isotopes of carbon and nitrogen including amino acid-specific isotope analyses were performed. Partial least squares regression (PLSR) models were applied to dioxins, PCBs, and mercury time series to examine how biological, ecological, and environmental factors (i.e., age, trophic diversity and position, temperature, salinity, proxies of cyanobacterial blooms and ultimate nutrient sources, abundance of relevant benthic fauna as well as biomass and size structure of the zooplankton community) contribute in explaining contaminant concentrations in herring, beyond atmospheric deposition (the main contaminant input in the Central Baltic basin). Our results emphasize that the contaminant burden in Baltic herring is significantly influenced by factors other than atmospheric deposition. Primarily, changes in herring’s trophic ecology, together with nitrogen-fixing cyanobacterial blooms (supporting both growth biodilution and bloom-induced dilution), were linked to dioxin, PCB, and mercury concentrations in fish. Our results support the need to consider all potential ecological synergies and linkages when managing a rapidly changing system such as the Baltic Sea, in order to minimize noxious blooms without compromising the positive impact on contaminant concentrations in fish.</p>