Sediments from 75 lakes in the Pyrenees mountain range have been sampled in the framework of the U.E. Project EMERGE. Contemporary (surface) and pre-industrial (15-17 cm depth) samples were taken from the sediment cores extracted at the deepest part of each lake, and these samples were analysed for total Fe, Al, Mn, Ti, Pb, Cd, Zn, As, Hg, and Se using aqua-regia digestion in a microwave oven followed by ICP-OS and ICP-MS. The analyses showed that the concentration of trace metals and metalloids is significantly high in the sediments of these relative remote, pristine lakes. As presents remarkably high concentrations in the Pyrenees. In general, more than 75% of lakes showed enrichment factors (EF) for most metals above 1.5, indicating the effect of atmospheric pollution on the mountain areas. The correlations among heavy metals in the surface sediments were stronger than for pre-industrial sediments, evidencing their common origin as pollutants in contemporary sediments, by opposition to lower correlations in pre-industrial sediments indicating the relative independence of their presence in the minerals of the catchments rocks. Maps are presented, showing the geographic distribution of trace metal and metalloid pollution over the Pyrenees: Central and Eastern Pyrenees clearly present higher pollution levels than the Western part.