Lake Ontario's condition has fluctuated since European settlement, and our understanding of the linkages between observed ecosystem shifts and stressors is improving. Changes in the physical and chemical environment of the lake due to non-indigenous species, pollution, sedimentation, turbidity, and climate change altered the pelagic primary producers, so algal assessments have been valuable for tracking long-term conditions. We present a chronological account of algal assessments to summarize past and present environmental conditions in Lake Ontario. This review particularly focuses on pelagic, diatom-based assessments as their fossils in sediments have revealed the combined effects of environmental insults and recovery. This review recaps the long-term trends according to three unique regions: Hamilton Harbour, the main lake basin, and the Bay of Quinte. We summarize pre-European impact settlement; eutrophication throughout most of the 20th century; subsequent water quality changes due to nutrient reductions; and filter-feeding dreissenid colonization and contemporary pelagic, shoreline, and embayment impairments. Recent data suggest that although phytoplankton biovolume is stable, species composition has shifted to an increase in densities of spring eutrophic diatoms and summer cyanobacteria. Continued monitoring and evaluation of historical data will assist in understanding and responding to the natural and anthropogenic drivers of Lake Ontario's environmental conditions.