Fish were sampled from 35 drainage and seepage lakes in the upper Michigan peninsula and Wisconsin in conjunction with Phase II of the U.S. Environmental Protection Agency's Eastern Lake Survey to explore the relationship between physicochemical characteristics of lakes and mercury concentrations in fish tissue. The lakes were selected using a stratified random design weighted for low pH to assess acidification effects on mercury bioaccumulation. Muscle tissue from yellow perch (Perca flavescens), northern pike (Esox lucius), white sucker (Catostomus commersoni) and largemouth bass (Micropterus salmoides) was analyzed for total and methylmercury. Differences in mercury concentrations were found between species, and methylmercury accounted for 99% of total mercury. Relationships were examined between tissue concentrations of mercury in yellow perch and lake physicochemical variables including pH, acid neutralizing capacity (ANC), calcium, conductivity, aluminum, total phosphorus, dissolved organic carbon, color, sulfate, lake area, lake depth, watershed area, Secchi depth and elevation. Mercury concentrations were negatively correlated with pH and ANC for both seepage and drainage lakes, but correlations with other water‐quality characteristics varied with lake type. Dissolved organic carbon had a negative correlation with fish mercury accumulation in seepage lakes, but not in drainage lakes. Mercury concentrations had a positive correlation with age, weight and length in yellow perch.

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