In the framework of the AL:PE 2 project, studies on acidification and organic pollution in mountain lakes have been conducted in several ranges in the Iberian peninsula: Pyrenees (Northeastern Spain), Sierra de Gredos (Central Spain), Sierra Nevada (Southern Spain) and Serra da Estrela (Central Portugal). These studies focused on water and sediment chemistry and organisms (benthic diatoms, Zooplankton, aquatic macroinvertebrates, and fish) as indicators of acidification. Organic micropollutants (PAH, PCB, DDE, hexachlorobenzene and others) in lake sediments and fish have been studied as tracers of atmospheric pollution. The Iberian peninsula lakes do not show severe anthropogenic acidification. pH values are in the range of sensitive lakes, but the levels of acidic pollutants are low. The status of the organisms surveyed agreed with this diagnosis. Pyrenean lakes showed the highest fluxes of organic pollutants related to fossil fuel combustion., higher pollutioninduced versus natural acidity ratios, and modeled alkalinity and pH declines.