Mercury (Hg) is a ubiquitous environmental contaminant that is transferred trophically through aquatic and terrestrial food webs. To better understand the routes of Hg uptake in organisms that rely on both aquatic and terrestrial food resources, we analyzed feather and down samples from nestling wading birds of varying trophic positions in both inland and coastal colonies. We used stable nitrogen and carbon isotope analyses to evaluate trophic positions of individual species (δ(15)N) and differences in foraging habitat use (δ(13)C). Inland, aquatic species had higher trophic status than the single terrestrial species examined, and the expected positive relationship between δ(15)N and Hg content of feathers was observed. However, the same was not true for all species from coastal colonies. Feathers from species that primarily consumed saltwater prey were relatively high in δ(15)N value and low in Hg content, which is opposite of the trend expected due to Hg biomagnification in food chains. In contrast, coastal species foraging in freshwater or a combination of freshwater and saltwater habitats displayed greater Hg contents in feathers. The apparent differential use of the two aquatic systems (freshwater and saltwater) in coastal environments by wading bird species results in variations in δ(15)N values and Hg contents in nestling feathers not found in species associated with only freshwater systems.