Legacy (i.e., polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecane (HBCDD)) and alternative halogenated flame retardants (HFRs) were analyzed in 31 whole fish samples from Lake Geneva in 2018. Two fish species, namely, the burbot (Lota lota) and the roach (Rutilus rutilus), were selected, hypothetically representing different habitats, feeding behaviors, and different metabolic capacities. Roach (N = 20) and burbot (N = 11) displayed similar size and mass, but the latter species was overall leaner than the former. The sum of individual PBDE concentrations (0.54–9.86 ng g−1 wet weight (ww)) was similar in both species, but the respective molecular profiles suggested contrasted metabolic capacities. HBCDD sum of isomer concentrations ranged from non-detected to 3.477 ng g−1 (ww), also similar in both species. Both PBDEs and HBCDD levels were far below the threshold that indicates a risk to fish predators. Referring to previous surveys, which involved a wider range of species, PBDE concentrations have declined or are stable. HBCDD concentrations remained low, despite the PBDE ban, which could have fostered the consumption of other HFRs. The occurrence of alternative HFRs was also low for most compounds analyzed. Only dechloranes and decabromodiphenyl ethane (DBDPE) had detection rates above 50%. Dechloranes spanned a concentration range between 5 and 10 times the quantification limits (0.002 to 0.005 ng g−1 wet weight), lower than DBDPE (< 0.005 to 2.89 ng g−1 wet weight). Quality standards targeting biota are currently missing for these emerging chemicals.