Nelligan C, Jeziorski A, Rühland KM, Paterson AM, Meyer-Jacob C, Smol JP. 2019. A multibasin comparison of historical water quality trends in Lake Manitou, Ontario, a provincially significant lake trout lake. Lake Reserv Manage. 36:243–259. Lake Manitou, on Manitoulin Island (Ontario, Canada), is a two-basin lake that supports a natural lake trout population and currently experiences late-summer hypolimnetic oxygen concentrations below the provincial criterion set to support this sensitive coldwater fish species. However, limited direct monitoring data make it difficult to assess long-term changes in hypolimnetic oxygen concentrations, and to identify what stressors may be responsible for those changes. Dated sediment cores from each basin of Lake Manitou were used to reconstruct end-of-summer volume-weighted hypolimnetic oxygen (VWHO) over the past ∼150 years using assemblages of sedimentary chironomid remains. To assess the influence of nutrients, regional warming, and lake browning, VWHO reconstructions were compared with sedimentary diatom assemblage changes, and spectrally derived trends in both sedimentary chlorophyll a (and its main diagenetic products) and sediment-inferred lakewater total organic carbon. The chironomid-inferred VWHO reconstructions suggest that deepwater oxygen concentrations are currently lower in both basins of Lake Manitou than they were prior to the 20th century (decreasing in the late 1880s coincident with the development of Manitoulin Island by European settlers). In both basins, post-1950 diatom assemblage shifts and whole-lake primary production (sedimentary chlorophyll a) trends suggest that increased nutrient inputs and warming-related changes (i.e., enhanced thermal stability) may be contributing to the current low-oxygen conditions of Lake Manitou. In the west basin, all paleolimnological proxies underwent more pronounced (and often earlier) changes than in the east basin, an observation that suggests more targeted management strategies may be needed to protect Lake Manitou’s coldwater fish population.