Because of the reduction in the use of polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecane (HBCD), novel brominated flame retardants (NBFRs), including 1,2-bis(2,4,6-tribromophenoxy) ethane (BTBPE), decabromodiphenyl ethane (DBDPE), hexabromobenzene (HBB), and pentabromoethylbenzene (PBEB), started to be marketed as alternatives to the banned formulations. In this study, the spatial distribution and accumulation of NBFRs, PBDEs, and HBCD in the biota have been investigated in the littoral compartment of a large and deep subalpine lake (Lake Maggiore, Northern Italy), using zebra mussel Dreissena polymorpha and roach (Rutilus rutilus) as bioindicators. To our knowledge, this is the first study reporting the contamination of NBFRs in the freshwater invertebrate D. polymorpha. Contamination of zebra mussel due to PBEB, HBB, and BTBPE was low, ranging from 0.9 to 2.9 ng/g lipid weight, from 1.1 to 2.9 ng/g l.w., and from 3.5 to 9.5 ng/g l.w., respectively. PBEB and BTBPE in roach were always below the detection limit, while the contamination of HBB ranged from < limits of detection (LOD) to 1.74 ng/g l.w., indicating a weak contamination. DBDPE was < LOD in all the considered biological samples. Finally, HBCD was detected in all organic tissues with mean concentrations up to 74.4 ng/g l.w. PBDE results, supported by principal component analysis elaboration, suggested a possible contamination due to the congeners composing the penta- and deca-BDE technical formulations, which are present in the Lake Maggiore basin. The biomagnification factor values showed that tetra- and penta-BDE biomagnified, while octa-, nona-, and deca-BDE were still bioavailable and detectable in the fish muscles, but they do not biomagnified. Considering the other BFRs, only HBCD showed a moderate biomagnification potential.