Samples of air (gas and particulate phases), bulk deposition, aquatic settling material and sediments were collected in Lake Maggiore (LM) in order to determine their content of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). Air (gas and particulate phases) concentrations were 0.5 pg m−3, 80 pg m−3, 13 pg m−3 and 106 pg m−3 for ΣPCDD/Fs, ΣPCBs, Σ dioxin-like PCBs (DL-PCBs) and ΣPBDEs, respectively. Deposition fluxes ranged from 0.7 ng m−2 d−1 for ΣPCDD/Fs to 32 ng m−2 d−1 for ΣPCBs. Aquatic settling material presented concentrations of 0.4 ng g−1 dry weight (dw) for ΣPCDD/Fs, 13 ng g−1 dw for ΣPCB, 3.4 ng g−1 dw for ΣDL-PCBs and 5.7 ng g−1 dw for ΣPBDEs. Mean sediment concentrations were 0.4 ng g−1 dw for ΣPCDD/Fs, 11 ng g−1 dw for ΣPCB, 3 ng g−1 dw for ΣDL-PCBs and 5.1 ng g−1 dw for ΣPBDEs. Similar PCDD/F and DL-PCB congener patterns in all the environmental compartments of LM point to an important, if not dominant, contribution of atmospheric deposition as source of these pollutants into LM. In contrast, PBDE congener distribution was not similar in the different environmental compartments. BDE 47 dominated air and settling material, while BDE 209 was the predominant congener in the bulk atmospheric deposition. Moreover, sediments showed two distinct PBDE congener profiles. Lower PBDE concentrated sediments were dominated by congeners 47 and 99, while BDE 209 dominated in higher PBDE concentrated samples. This suggests the influence of local sources as well as atmospheric input of PBDEs into LM.