The Baltic herring (Clupea harengus membras) is an ecologically and economically important species of forage fish that plays a central role in the Baltic Sea food web. While elevated concentrations of contaminants within biota have been well documented in this historically polluted sea area, the effects that ecosystem changes such as eutrophication, climate-driven shifts in food web structure, and changes in growth have on contaminant burden remain poorly understood. This thesis investigates the complex effects of changing trophic interactions (Studies I, II, & III) and growth (Study III) on contaminant burden in herring, while providing updated tools to investigate similar questions in the future (Study IV). Study I showed that concentrations of persistent organic pollutants (PCBs and PCDD/Fs) and heavy metals (Hg) in herring are best explained by ecological and trophic changes, rather than decreased emissions. Higher cyanobacterial bloom intensity was associated with decreases in contaminant concentrations. Study II further investigated the relationship between herring and cyanobacteria by using compound specific isotope analysis in amino acids to quantify the amount of diazotrophic-N fixed by cyanobacteria present in juvenile herring over a growth season. Results showed that at peak levels, more than 30% of N in juvenile herring was fixed by cyanobacteria, with levels correlated to cyanobacterial biovolume in the water. Study III analyzed concentrations of PCDD/Fs and PCBs in the same juvenile herring used in study II and investigated the variables driving differences in concentrations. It was observed that contaminant concentration significantly decreased with fish size, with the smallest juveniles having higher contaminant concentrations than adults. General additive models showed that growth rate, assessed from daily growth rings in otoliths, was the variable most responsible for changes in contaminant concentration, with a higher growth rate leading to lower contaminant concentrations. These three studies show that cyanobacteria blooms in the Baltic have possible positive effects including providing N to the production of fish resources thereby potentially improving growth conditions and reducing contaminants through somatic growth dilution. Since non-lethal estimates of in-situ growth rates are difficult, we further developed a bioenergetic model for juvenile herring using ambient zooplankton densities and a functional consumption response, and incorporated water temperature and light period to predict growth (Study IV). The model was shown to better predict natural growth than previous models. The work in this thesis shows that ecosystem changes thought to be detrimental, such as increased cyanobacterial blooms, can have interactions with contaminant burden that are beneficial (Studies I & II), while showing that if the growth of juvenile herring can be improved, contaminant burden can be decreased (Study III). Lastly, a new mathematical method to calculate the important metric of growth rate in juvenile herring is presented, which will allow for future predictions of herring growth in a warming Baltic Sea (Study IV). In conclusion, all four studies support the need to contemplate potential ecological synergies and linkages when managing a rapidly changing system, in order to minimize the potential harmful effects of changes such as eutrophication, without compromising the positive impact on contaminant concentrations in fish.