To establish a relationship between levels of atmospheric pollutants such as SO2 and the acid-base chemistry of lakes is an important but elusive goal of studies on acid precipitation. But the direct effect of acid deposition on the acid-neutralizing capacity (ANC) of lake waters is difficult to isolate, because rates of change of the latter are small1 and ANC is also influenced by other factors2,3. We report here the observation of changes in the ANC of a seepage lake in Michigan driven by the effects of drought on the local hydrology. While levels of acidic wet deposition at the lake remained at a constant, moderate level over a five-year period, a rapid, major loss of ANC occurred because of changes in the input of ANC-rich groundwater. Thus even modest climate fluctuations can have substantial effects on lake chemistry, and must be taken into account when interpreting temporal trends. Sustained drought conditions might similarly alter the acid-base chemistry of other softwater systems.