In the middle of Europe, the Alps form a geographical and meteorological trap for atmospheric pollutants including volatile and semi-volatile organic compounds emitted in the surrounding lowlands. This is due to their barrier effects, high precipitation rates, and low ambient temperatures. Also the pollutants emitted in the cities inside the Alps spread in the region depending on orographic and meteorological conditions. Although a number of studies on the distribution and effect of pollutants in the Alps has been published, comprehensive information on potential hazards, and ways to improve this sensible environment are lacking. This opinion paper is the result of a discussion during the Winterseminar of the AlpsBioCluster project in Munich. It summarizes the current literature and presents some case studies on local pollution sources in the Alps, and the possibility of using biomonitoring techniques to assess critical pollution loads and distributions.