Yearling yellow perch were collected from sixteen Muskoka-Haliburton lakes to determine interrelationships between water quality, Hg residues in fish and fish condition. The lakes studied were Precambrian shield lakes with a pH range of 5.6 to 7.3 and total inflection point alkalinities of 0.4 to 16.0 mg L−1. Mercury residues in yellow perch ranged from 31 to 233 ng g−1 and were inversely correlated (p < 0.001; r = 0.84) with lakewater pH. Stepwise linear regression analyses selected lakewater pH as the only significant parameter associated with Hg accumulations. Alkalinities, sulphate, Ca and dissolved organic carbon (DOC) were not selected as significant. Likewise, lakewater pH and Hg residues in yellow perch were inversely (p < 0.001) correlated with fish condition. Lakewater pH, accounted for 74% and Hg in fish a further 11% of the variability in fish condition. Terrestrial drainage size/lake volume ratios were also correlated (p < 0.05; r = 0.78) with Hg accumulations in perch from a subset of nine headwater lakes. No temporal trends in Hg residues were evident in yellow perch over a 9 yr interval (1978–1987).