Classic (polybromodiphenyl ethers, PBDEs) and emerging halogenated flame retardants (HFRs) such as decabromodiphenyl ethane (DBDPE) and halogenated norbornenes, as well as organophosphate flame retardants (OPFRs) were analysed in 52 sediments and 27 fish samples from three European river basins, namely the Evrotas (Greece), the Adige (Italy) and the Sava (Slovenia, Croatia, Bosnia and Herzegovina and Serbia). This is the first time that FR levels have been reported in these three European river basins. The highest contamination was found in the Adige and Sava rivers, whereas lower values were obtained for the Evrotas. The levels in sediment samples ranged between 0.25 and 34.0ng/g dw, and between 0.31 and 549ng/g dw, for HFRs and OPFRs respectively. As regards levels in fish, concentrations ranged between 9.32 and 461ng/g lw and between 14.4 and 650ng/g lw, for HFRs and OPFRs, respectively. Thus, whereas OPFR values were higher in sediments, similar concentrations (in the Evrotas) and even lower concentrations than HFRs (Sava) were found for OPFRs in the fish samples, indicating the lower bioaccumulation potential of OPFRs. Biota to sediment accumulation factors (BSAFs) were calculated and higher values were obtained for HFRs compared to those assessed for OPFRs.