This list is arranged by drainage basin, with respective tributaries indented under each larger stream's name.

Aegean Sea edit

• Vardar
  • Treska
    • Golema Reka
  • Lepenac
    • Nerodimka
  • Kadina River
  • Pčinja
    • Kriva Reka
    • Kumanovska Reka
  • Topolka
  • Babuna
    • Crnička Reka
  • Bregalnica
    • Zrnovska Reka
    • Lakavica
    • Otinja
  • Crna Reka
    • Šemnica
    • Dragor
    • Raec
  • Bošava
    • Dosznica
  • Stragarnica
  • Anska Reka
  • Konska Reka
  • Pena
• Struma (in Bulgaria)
  • Lebnica
  • Strumica
    • Stara Reka

Adriatic Sea edit

• Drim (in Albania)
  • Black Drin
    • Sateska
      • Golema Reka
    • Radika
      • Derven
      • Ribnička
        • Dlaboka

Black Sea edit

• Danube (in Serbia)
  • Južna Morava (in Serbia)
    • Binačka Morava