Pb-210-dated sediment cores and surface sediments from Lake Chapala (LC), Mexico, were analyzed to assess the temporal trends in concentrations and fluxes of persistent organic pollutants (POPs: PAHs, PCBs and PBDEs). Total sediment concentrations of PAHs (95-1,482 ng g(-1)), PCBs (9-27 ng g(-1)) and PBDEs (0.2-2.5 ng g(-1)) were indicative of moderate to intense contamination. The POP concentrations have progressively increased since the 1990s. The light molecular weight PAHs, and the prevalence of PCB congeners with low-chlorination levels (e.g., di- to tri-CB) and low-to medium-brominated (tri- to penta-BDE) PBDEs in most sections of the sediment profiles, suggested that these POPs have most likely reached these sediments by long-range atmospheric transport from distant sources; although the significant presence of heavier PAH, PCB and PBDE congeners in the topmost sediments, indicate that other nearby and local sources (soil erosion from the catchment, urban and industrial wastewaters discharges, as well as navigation) might have also contributed to the recent input of POPs to LC. Taking into account the relevance of LC as regional freshwater supply and commercial fishing ground, the potential risk posed by the organic contaminated sediments to the biota and human population should not be underestimated.