We present a case study comparing metrics of methylmercury (MeHg) contamination for four undeveloped lakes in Voyageurs National Park to wet atmospheric deposition of mercury (Hg), sulfate (SO4–2), and hydrogen ion (H+) in northern Minnesota. Annual wet Hg, SO4–2, and H+ deposition rates at two nearby precipitation monitoring sites indicate considerable decreases from 1998 to 2012 (mean decreases of 32, 48, and 66%, respectively). Consistent with decreases in the atmospheric pollutants, epilimnetic aqueous methylmercury (MeHgaq) and mercury in small yellow perch (Hgfish) decreased in two of four lakes (mean decreases of 46.5% and 34.5%, respectively, between 2001 and 2012). Counter to decreases in the atmospheric pollutants, MeHgaq increased by 85% in a third lake, whereas Hgfish increased by 80%. The fourth lake had two disturbances in its watershed during the study period (forest fire; changes in shoreline inundation due to beaver activity); this lake lacked overall trends in MeHgaq and Hgfish. The diverging responses among the study lakes exemplify the complexity of ecosystem responses to decreased loads of atmospheric pollutants.