The whitemouth croaker (Micropogonias furnieri) is one of the most commercially important species along the Atlantic coast of South America. Moreover, some of its biological traits (long life span, inshore feeding, high trophic position) make this species a suitable sentinel of coastal pollution. Here, we investigated contamination by multiple legacy and emerging organic pollutants, such as brominated and chlorinated flame retardants, polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs), in whitemouth croakers from two estuaries (Guanabara and Sepetiba Bays) located in industrialized and urbanized areas in Rio de Janeiro State, Southeastern Brazil. Furthermore, we assessed how biological and ecological features could explain the observed contamination patterns. Regarding brominated flame retardants, concentrations of polybrominated diphenyl ethers (PBDEs) varied from 7.6 to 879.7 pg g−1 wet weight (w.w.), with high contribution of tetra-, penta-, hexa- and deca-BDEs. The sum of chlorinated flame retardants (dechlorane-related compounds, ΣDRC) ranged from <LOD to 41.1 pg g−1 w.w., mostly represented by Dechlorane 603 and Dechlorane Plus (DP). Concentrations of PCDDs and PCDFs varied from <LOD to 1.7 pg g−1 w.w., while the Toxic Equivalent (TEQ-PCDD/Fs) levels ranged from 0.1 to 0.2 pg g−1 w.w. Positive correlations between δ15N and concentrations of tri-, tetra- and penta-BDEs, as well as ΣDRC, DP and anti-DP isomers suggested that ecological factors (namely biomagnification along the food web) influence contamination of whitemouth croakers in the estuaries studied. Moreover, the sum of PBDEs (ΣPBDE), tri- and tetra-BDEs concentrations were negatively correlated with fish size, suggesting that depuration by fishes and/or habitat shift throughout the whitemouth croaker's life cycle might also influence concentrations. Overall, our study emphasized the need for further investigations to help understand the complex patterns of bioaccumulation and biomagnification that seem to exist in Southeastern Brazil.