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Mercury (Hg) contamination is considered a global concern for humans and wildlife, and although the number of studies dealing with that issue continues to increase, some taxonomic groups such as small passerine birds are largely understudied. In this paper, concentration of mercury in the aquatic warbler (Acrocephalus paludicola) feathers, a globally threatened passerine species, was examined. The concentration differences between two ages and sexes were investigated. The comparison of feathers taken on autumn migrants of two age categories act as a comparison of the species’ exposure within the two different areas (European breeding or African wintering grounds). The average Hg concentration for all sampled individuals [2.32 μg/g dw (range 0.38–12.76)] is relatively high, compared with values found in other passerine species. An age difference was found, with first-year individuals displaying higher mercury concentrations than adults. This indicates that birds are exposed to mercury pollution during the breeding season, i.e., in the continental floodplains of eastern Europe. The average Hg concentration in feathers grown on the breeding grounds was 3.88 ± 2.59 μg/g dw, closer to the critical value of 5 μg/g dw, which is considered to impair the health of individuals. The findings suggest that mercury pollution may constitute a threat so far neglected for the endangered aquatic warbler.