The conservation of migratory species poses significant challenges that may be countered by detailed knowledge about the sites used by migrants throughout the annual cycle. We present the first GPS-tracking data on the migration of declining Caspian terns Hydroprogne caspia breeding in the Baltic Sea. For 39 Caspian terns from colonies along a latitudinal gradient from 57 to 65°N, we identified key migratory routes, stopovers and wintering areas. In autumn these seabirds migrated using coastal and freshwater stopovers along six routes to reach their wintering areas across the Sahel, the Nile River Basin and the southern Iberian Peninsula. In spring, adults returned to the breeding grounds in the Baltic using a time optimizing strategy by reducing time at stopover by 78%, whereas most subadults remained sedentary and some performed only partial return migrations. Of the stopover sites used in both seasons, 58% are protected and have a reported management plan. Conservation strategies in wintering areas, stopover sites that are not protected or had not been previously recognized, and the inclusion of the species in important migratory flyways across Europe and Africa will be important to prevent further population declines of a species that depends on aquatic habitats.