Bulgaria has a unique geographic position in Europe, with two migratory wild bird routes, Via Pontica and Via Aristotelis, passing through the country. Via Pontica is the second-largest migration route in Europe, with hundreds of thousands of birds, representing more than 110 species, wintering in lakes by the Black Sea and the wetlands near the Danube River. Via Aristotelis is situated in West Bulgaria along the Strouma and Mesta river valleys, and it is of regional importance for the Balkan Peninsula. In this study, we examined more than 2000 samples from wild birds from the orders Anseriformes, Ciconiiformes, Gruiformes, and Charadriformes in the period 2006–2008. We isolated three influenza viruses, subtypes H4N6, H7N7, and H10N7, all from mallards, Anas platyrhynchos. The H7N7 was isolated from a hunter-killed mallard at the river bank of Kamchia (Via Pontica). The cleavage site sequence of the hemagglutinin gene in the H7N7 isolate was PEIPKGR*GLF, which is characteristic of a low-pathogenic virus. The H4N6 isolates belonged to a mallard wintering along the Maritza River (Via Aristotelis). We detected the H10N7 virus in samples from mallards that inhabit the Ogosta River, one of the feeders of the Danube (Via Pontica). All these viruses were detected during the active migration of the birds, February–March.