At a high mountain lake in catchments of mica schist and gneiss rock in the European Alps, substantial increases in solute concentrations of sulfate, magnesium, calcium, silica, manganese, and nickel were observed over the past two decades. We hypothesized that microbial interactions with rock in the catchment of the lake might play an important role. We studied the chemolithotrophic activities resulting in the production of metal mobilizing metabolites (mineral acids). The potential of nitrifying and sulfur-oxidizing cultures derived from rock to mobilize elements from this rock when augmented with ammonium and thiosulfate was investigated in a 35 day laboratory study. Bacterial species prevailing in the indigenous nitrifying and sulfur-oxidizing mixed cultures were determined by 16S rRNA gene sequence based analysis. The average mineralogical composition of the rock sample was quartz (50%), feldspar (27%), muscovite (15%), chlorite (6%), and dolomite (2%). The increase of each soluble element in the presence of cultures relative to the conditions without microbes was related to the total element in the rock sample (leaching efficiency in percent). After 35 days, leaching efficiency was 7% (Ca), 2.4% (Mg), and 6.3% (Mn) in the presence of the nitrifying culture. In the presence of the sulfur-oxidizing culture, leaching efficiency was 13% (Ca), 5.7% (Mg), 5.4% (Mn), 1.3% (Zn), 0.2% (Fe), and 0.1% (Al). The results suggest that under conditions of abundant substrate availability, chemolithotrophic activity on catchment rock can contribute to the increase in soluble Ca, Mg, and Mn in lake water.