During the past few decades there has been a growing concern over the influence of human activities on local, regional, and global environments. Much attention has focused on environmental changes in the Great Lakes watershed because the region is heavily populated and economically dependent on the lakes. Many efforts have been made to restore the health of Great Lakes ecosystems and to better manage future changes. In order to accurately project future trophic states a full knowledge of past natural variability is required. In order to temporally extend historical records (last ~200 yrs) of trophic conditions, we have collected a series of relatively long (~ 5 m) sediment piston cores from the Rochester Basin in order to develop a record of paleoproductivity over the past 11,200 cal yrs BP. We used a multiproxy approach, focusing on stable isotope values of calcite and organic matter. d¹³C values of calcite and d¹³C and d¹⁵N values of organic matter indicate that historic (last 200 yrs) levels of primary productivity have been unprecedented during the past 11,200 yrs. A period of moderate primary productivity and calcite precipitation occurred between ~11.2 ka to ~9.9 ka yrs during the Post-Younger Drays Climate Interval. Primary productivity and calcite precipitation were closest to their historic values between ~9.6 ka to ~6.0 ka yrs ago when summer temperatures were 2-3°C warmer. Warmer summers resulted in increased chemical weathering, nutrient supply, and longer thermal stratification, which increased the duration of primary productivity and the abundance of picoplankton. The combination of these factors resulted in increased calcite precipitation. A major change in the lake's limnology occurred ~ 4.3 ka yrs ago represented by an increase in biogenic silica from < 1% to modern day values of ~ 6%, as well the disappearance of calcite which does not return until historic time. The changes in the lake's limnology were related to decreased temperatures and the return of Upper Great Lakes drainage. These data suggest that the trophic state of Lake Ontario has varied in the past due to natural forcing and will likely do so in the future.