On the western coast of North America, several estuaries provide shorebirds with important winter and stopover habitat. These habitats include not only aquatic estuarine resources but also adjacent upland agricultural lands. The extent to which shorebirds use estuarine vs. upland habitats at these stopover sites is difficult to quantify but crucial to designing strategies for their conservation. We measured stable isotopes (δ¹³C, δ¹⁵N) in whole blood of Dunlins (Calidris alpina) and their prey from two major estuaries in north Puget Sound, Washington, USA, to estimate their relative use of estuarine vs. upland agricultural zones. We identified four isotopically distinct dietary inputs (agriculture high in ¹⁵N, other agriculture, marsh/marine, and freshwater plume). Isotopic sampling and modeling was informed by movements and habitat use derived from radiotelemetry. This isotopic structure allowed us to conclude that these Dunlins obtained about 62% of the protein in their diet from agricultural lands and 38% from the estuary. Our results underline the urgent need to combine management of estuaries and upland agricultural areas in strategies for shorebird conservation.