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Freshwater fish in several regions of New York State (NYS) are known to contain concentrations of mercury (Hg) associated with negative health effects in wildlife and humans. We collected blood and breast feathers from bald eagle (Haliaeetus leucocephalus) nestlings throughout NYS, with an emphasis on the Catskill region to determine their exposure to Hg. We assessed whether habitat type (lake or river), region (Delaware–Catskill region vs. rest of NY) or sample site elevation influenced Hg concentrations in bald eagle breast feathers using ANCOVA. The model was significant and accounted for 41% of the variability in log10 breast feather Hg concentrations. Mercury concentrations in nestling breast feathers were significantly greater in the Delaware–Catskill Region (geometric mean: 14.5 µg/g dw) than in the rest of NY (7.4 µg/g, dw), and greater at nests located at higher elevations. Habitat type (river vs. lake) did not have a significant influence on breast feather Hg concentrations. Geometric mean blood Hg concentrations were significantly greater in Catskill nestlings (0.78 µg/g ww) than in those from the rest of NY (0.32 µg/g). Mercury concentrations in nestling breast feathers and especially blood samples from the Delaware–Catskill region were generally greater than those reported for most populations sampled elsewhere, including areas associated with significant Hg pollution problems. Bald eagles can serve as valuable Hg bioindicators in aquatic ecosystems of NYS, particularly given their broad statewide distribution and their tendency to nest across all major watersheds and different habitat types.