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Changes in the far north of Ontario (>50°N latitude), like climate warming and increased industrial development, will have direct effects on watershed characteristics and lakes. To better understand the nature of remote northern lakes that span the Canadian Shield and Hudson Bay Lowlands, and to address the pressing need for limnological data for this vast, little-studied area of Ontario, lake chemistry surveys were conducted during 2011-2012. Lakes at the transition between these physiographic regions displayed highly variable water chemistry, reflecting the peatland landscape with a mix of bog and fen watersheds, and variations in the extent of permafrost. In the transition area, Shield and Lowlands lakes could not be clearly differentiated based on water chemistry; peat cover decouples, to varying degrees, the lakes from the influences of bedrock and surficial deposits. Regional chemistry differences were apparent across a much broader area of northern Ontario, due to large-scale spatial changes in geology and in the extent of peatlands and permafrost. Shield lakes in the far northwest of Ontario had Ca, Mg, and TP concentrations markedly higher than those of many Lowlands lakes and previously studied Shield lakes south of 50°N, related to an abundance of lacustrine and glacial end-moraine deposits in the north.