Annual freshwater quality monitoring data for 20 lakes across Canada. Parameters include total mercury, methylmercury, pH, alkalinity, specific conductance, colour, chlorophyll, nutrients, ions, dissolved inorganic and organic carbon, and total metals. In most years surface samples were collected from three locations on each lake, following nationally standardized protocols. Sampling occurred from 2008 to 2016, with six core lakes sampled throughout the eight-year period. In all years except 2009 samples were collected in the fall, before lake turnover. In 2009 samples were collected after lake turnover.