Chickaloon Flats, Kenai National Wildlife Refuge, is an 11,000-ha tidal mudflat complex in upper Cook Inlet, Alaska. One-third (23 of 70) of Alaskan shorebird species use this protected coastal estuary stopover during migration. We conducted an isotopic approach to estimate probable breeding, staging and/or non-breeding origins of six shorebird species, some of high conservation concern, using Chickaloon during spring and fall migration of 2009 and 2010. We analyzed stable-hydrogen (δ²H), carbon (δ¹³C), and nitrogen (δ¹⁵N) isotope ratios from feathers and performed a likelihood-based assignment to infer North and South American origins. Estimated molting distributions for Greater Yellowlegs (Tringa melanoleuca) occurred in southwest Alaska, and south-central Alaska for Short-billed Dowitcher (Limnodromus griseus caurinus). Lesser Yellowlegs (Tringa flavipes) likely molted in western Alaska and a latitudinal band across Canada and wintered throughout the contiguous United States. Least Sandpipers (Calidris minutilla) wintered from Oregon and south in North America but showed an isotopically similar possibility in Ecuador, Colombia, and Venezuela. Long-billed Dowitchers (Limnodromus scolopaceus) molted primaries across western United States and Canada. Pectoral Sandpipers (Calidris melanotos) likely molted near Rio de La Plata in southeastern South America. These results highlight the overall value of Chickaloon Flats as a stopover for long-distance shorebird migrants.