Despite PCBs being banned since the 1980's, some European peri-alpine lakes, and consequently their fish populations, are still contaminated by these xenobiotics. We investigated the relative contribution of physiological and trophic factors that could be implicated in fish PCB bioaccumulation in Lake Bourget (France), one of the most contaminated in Europe, by collecting Arctic char (n = 55) and European whitefish (n = 89) from 2013 to 2016. Concentrations of 7 indicator PCBs were 9-168 ng.g w.w-1 in whitefish and 90-701 ng.g w.w-1 in Arctic char. The fish trophic positions calculated from δ 15N values were positively correlated with PCB concentrations (r2 = 0.45; p < 0.001). A biomagnification model relying on TP and lipid content of fish was then designed, and it confirmed this result. A Bayesian mixing model based on δ 13C and δ 15N values was used to estimate the relative contribution of preys in the fish diet, which explained a significant proportion of the biomagnification model residuals (i.e., 17%). Zooplankton consumption was negatively correlated with PCB concentrations, whereas consumption of chironomids enhanced the PCB burden in fish. Correction of the biomagnification model for individual diets of fish increased the correlation between the predicted and measured fish PCB contents (R2 = 0.71; p < 0.001), highlighting the importance of fish feeding habits in the bioaccumulation process.