© 2016, © Copyright by the North American Lake Management Society 2016. Nelligan C, Jeziorski A, Rühland KM, Paterson AM, Smol JP. 2016. Managing lake trout lakes in a warming world: A paleolimnological assessment of nutrients and lake production at three Ontario sites. Lake Reserve Manage. 32:315−328. Recent declines in hypolimnetic dissolved oxygen (DO) concentrations in many lakes throughout Ontario have prompted concern regarding the health of lake trout (Salvelinus namaycush) populations. We used diatom assemblages and spectrally inferred chlorophyll a from the dated sediments of 3 lake trout lakes to track trends in total phosphorus (TP) and whole-lake production over the past ∼150 years. Eagle Lake is considered a sensitive lake trout lake because DO concentrations have been lower than the provincial standard (>7 mg/L) since the early-2000s; however, a lack of monitoring data impedes the evaluation of current conditions within a historical context. For a regional perspective, we compared trends in Eagle Lake with those of 2 additional lake trout lakes ∼200 km away. The diatom assemblages of Eagle Lake underwent a shift in the early-1980s, marked by a decline in the relative abundance of Stephanodiscus minutulus and an increase in small Cyclotella (sensu lato) taxa. This change is indicative of nutrient reductions and is consistent with a decline in both monitored and diatom-inferred TP. Sedimentary chlorophyll a peaked after the 1980s, suggesting whole-lake production has increased independent of nutrient loading, likely due to regional warming and a longer growing season. Diatom compositional changes at the 2 other sites are indicative of climate warming, with increases in the relative abundance of Discostella stelligera and spectrally inferred chlorophyll a. Our data suggest climate is likely the dominant driver of the observed algal changes, highlighting that the effects of warming on habitat quality should be considered in lake management strategies.