Historical changes in Holocene climate in northeastern Ontario were quantified using analyses of sedimentary pollen, diatoms, and pigments in a small boreal lake. Modern analog reconstructions of average temperature from Holocene pollen assemblages of Charland Lake showed temperature was ~2°C warmer than present conditions ~7800–4500 cal. yr BP, a time period consistent with the Holocene thermal maximum (HTM). Pollen data suggest a two-phase HTM: warm and dry conditions based on the presence of primarily Pinus spp., followed by warm and wet conditions based on increases in cedar. Overall, algal production was low during the HTM, as reflected by low concentrations of pigments and diatoms. In the late HTM, increases in cedar pollen and planktonic diatoms suggest sustained increases in water levels for the remainder of the Holocene. During the Post-HTM Period (~4500–2000 cal. yr BP), a period that was warmer than today but cooler than the HTM, overall pigment production was significantly higher than all other periods. However, changes in diatom species composition suggest this period was not uniform, with variation occurring between diatoms indicative of higher and lower nutrient levels. The last ~2000 cal. yr BP was less productive than the Post-HTM Period but more productive than the HTM with higher production from diatoms and cyanobacteria. This study suggests that the relationship between climate and lake water production can be quite complex, and that changes in temperature, precipitation, light, lake levels, and mixing patterns are among factors that are related to changes in subfossil phototroph assemblages.