The concentrations of polybrominated dibenzo-p-dioxins (PBDDs) and polybrominated methoxylated diphenyl ethers (MeO-PBDEs) were investigated in perch (Perca fluviatilis) collected from a Baltic Sea background contaminated area between 1990 and 2005. No temporal trend was found, but large variations were observed - up to 5-fold and 160-fold differences in MeO-PBDE and PBDD concentrations, respectively - between consecutive years, suggesting that retention of these compounds, particularly the PBDDs, is limited. Examination of the congener profiles using principal component analysis (PCA) and correlation analysis indicated that MeO-PBDEs without adjacent substituents (6-MeO-BDE47) or with two adjacent substituents (2'-MeO-BDE68 and 6-MeO-BDE90) are retained more than MeO-PBDEs with three adjacent substituents (6-MeO-BDE85 and 6-MeO-BDE99) and that 1,3,6,8-tetraBDD and 1,3,7,9-tetraBDD are retained more than the other PBDDs which have vicinal hydrogen. Debromination could explain the limited retention of 6-MeO-PBDE85 and 6-MeO-BDE99 and the absence of 2-MeO-BDE123 and 6-MeO-BDE137, and cytochrome P-450 mediated oxidation could explain the limited retention of PBDDs containing vicinal hydrogen. The levels of organobromines, especially MeO-PBDEs, were found to covary with water conditions related to primary production, for example temperature, depth visibility, and inorganic nutrient concentrations, which also favor fish productivity. The results suggest natural production of MeO-PBDEs and PBDDs and imply that they fluctuate considerably over time, as do common marine toxins in fish. Thus, assessments of human and environmental risk should consider both the average and peak concentrations of these contaminants in marine biota.