Paleoecological analysis of the sediment record of 12 Adirondack lakes reveals that the 8 clearwater lakes with current pH<5.5 and alkalinity <10 microeq/l have acidified recently. The onset of the acidification occurred between 1920 and 1970. Loss of alkalinity, based on quantitative analysis of diatom assemblages, ranged from 2 to 35 microeq/l. The acidification trends are substantiated by several lines of evidence including stratigraphies of diatom, chrysophyte, chironomid, and cladoceran remains, Ca:Ti and Mn:Ti ratios, sequentially extracted forms of Al, and historical fish data. Acidification trends appear to be continuing in some lakes, despite reductions in atmospheric sulfur loading that began in the early 1970s. The primary cause of the acidification trend is clearly increased atmospheric deposition of strong acids derived from the combustion of fossil fuels. Natural processes and watershed disturbances cannot account for the changes in water chemistry that have occurred, but they may play a role. Sediment core profiles of Pb, Cu, V, Zn, S, polycyclic aromatic hydrocarbons, magnetic particles, and coal and oil soot provide a clear record of increased atmospheric input of materials associated with the combustion of fossil fuels beginning in the late 1800s and early 1900s.