El Molino River (Rio El Molino) is the name of two medium streams in El Salvador.

• 13°15′47″N 88°27′00″W / 13.262973°N 88.449974°W / 13.262973; -88.449974 (Rio El Molino, Jiquilisco Bay), near the Jiquilisco Bay in Usulután District.

• 13°57′N 89°57′W / 13.950°N 89.950°W / 13.950; -89.950 (Rio El Molino, Ahuachapan), near the city of Ahuachapán in Ahuachapán District.

Both streams have at least large to moderate quantities of fresh water year round, especially from early May through October.