Two small high mountain lakes in the Alps were monitored in 1984-2003 to follow their response to changes in human impact, such as deposition of atmospheric pollutants, fish stocking and climate change. The results were compared to occasional samplings performed in the 1940s, and to the remains found in sediment cores. When monitoring started, the most acid-sensitive of them, Lake Paione Superiore, was acidified, with evident effects in its flora and fauna: benthic diatoms assemblage was shifted towards acidophilous species, and zooplankton lost the dominant species, Arctodiaptomus alpinus. Palaeolimnological studies outlined that lake acidification paralleled the increasing input of long-range transported industrial pollutants, traced by spherical carbonaceous particles. On the contrary, the biota of Lake Paione Inferiore appeared to be mainly affected by fish stocking. In the last twenty years, decrease in acid load from the atmosphere led to an improvement in lake water quality, with an increase in both pH and alkalinity. First signs of biological recovery were identified, such as change in diatom flora and appearance of sensitive species among benthic insects. However, climate change and episodic deposition of Saharan dust were important driving factors controlling lake water chemistry. Further monitoring to assess the effects of climate change and of the increasing load of nitrogen and other pollutants is recommended.