Sediment analysis in three Italian subalpine lakes, very close to each other and exposed to different anthropogenic pressure, was used to assess the risk from organic pollutants, including some very persistent and widespread micropollutants (PCB, DDT, PAH) as well as known local pollutants. Additionally, a wide-spectrum characterization of organic compounds by GLC-MS analysis allowed the detection of other classes of chemicals. The contamination levels were related to long distance transport and to local sources of pollution in the watershed. PAH, PCB and organochlorine pesticide levels agree with the load calculated from atmospheric depositions. Local sources of pollution are responsible for the contamination by aliphatic hydrocarbons and tris(monochloroisopropyl)-phosphate (TCIPP); these compounds were found only in the two most urbanized basins. Heavy contamination by TCIPP was found in both water and sediments; water concentrations are considered hazardous for drinking purposes. This study shows that local contaminants, not yet included in any priority list, may single out as a major environmental concern.