Alpine areas in north-western Italy are subject to high deposition of atmospheric pollutants. Chemical investigations on high-altitude lakes indicate that most of them are recovering from acidification; however, they are still affected by the deposition of pollutants from the atmosphere, especially of heavy metals. This study compares the concentrations of heavy metals in alpine lake waters with those found in atmospheric depositions, to identify the possible contribution of deposition inputs to surface water ecosystems. The results were analysed by multivariate statistical techniques to identify the main emission sources of the various metals. Levels of trace metals in alpine lakes are generally low, and bedrock and surficial geology proved to be a major factor controlling metal concentrations in lake water. In fact, terrigenous elements show a wide range of concentrations while metals of anthropogenic origin, such as lead and cadmium, are often below the detection limits of the method; chrome and nickel are also present in very low concentrations. The median values of heavy metals in Italian alpine lakes are similar to those found in other lake surveys performed in remote areas, especially as regards metals of anthropogenic origin. The Visual MINTEQ model was applied to long-term chemical data of selected alpine lakes, to calculate aluminium speciation and to simulate its change in response to gradual modifications in a unit of pH. The ultimate aim of the modelling was to evaluate the possible threat to aquatic organisms of these highly toxic compounds.