Freshwater ecosystems are increasingly affected by human influences. Since the pre-industrial era, lakes of the Muskoka-Haliburton region of south-central Ontario have had increases in shoreline residential development and acid deposition. Previous research on 54 of these lakes, using sediment cores and diatom-based transfer functions, showed changes in lakewater pH and total phosphorus concentration between the preindustrial era and 1992. Since 1992, there has been further change, which we have documented for the same set of lakes, using similar methods. For example, dissolved organic carbon has increased and there have been significant increases in planktonic diatoms (e.g. Cyclotella stelligera) commonly associated with climate warming. More striking diatom changes have occurred in the past 15 years than between pre-industrial times and 1992. Significant changes observed in both chemical (e.g. pH, Ca, DOC) and biological data suggest that novel stressors, such as declines in lake calcium concentrations, acting in conjunction with climate and land-use change, have created ecosystems for which there are no historical analogs. © 2012 Springer Basel.