Anthropogenic inputs of mercury (Hg) into the environment have significantly increased in the past century. Concurrently, the availability of methylmercury (MeHg) in aquatic systems has increased to levels posing risks to ecological and human health. We use the common loon (Gavia immer) as an upper trophic level bioindicator of aquatic Hg toxicity in freshwater lakes. Multiple endpoints were selected to measure potential negative impacts from MeHg body burdens on behavior, physiology, survival and reproductive success. A robust spatio-temporal dataset was used that included nearly 5,500 loon Hg measurements over an 18-year period. We measured significant changes related to elevated MeHg body burdens, including aberrant incubation behavior, lethargy, and wing area asymmetry. Mercury body burdens in adult loons increased an average of 8.4% per year. Increasing Hg body burdens reduced the number of fledged chicks per territorial pair, with highest risk loons producing 41% fewer fledged young than our reference group. Our multiple endpoints establish adverse effect thresholds for adult loons at 3.0 ug/g (wet weight) in blood and 40.0 ug/g (fresh weight) in feathers. Mercury contamination in parts of Maine and New Hampshire is a driving stressor for creating breeding population sinks. Standardized monitoring programs are needed to determine if population sinks occur elsewhere and to track aquatic ecosystem responses to changes in Hg emissions and deposition.