Goes from estuary to source, by the sound of things, from this Levantine city (6)
I believe the answer is:
beirut
'city' is the definition.
(Beirut is an example)
I don't understand how the rest of the clue works.
Can you help me to learn more?
(Other definitions for beirut that I've seen before include "Capital city of Lebanon" , "Middle East capital" , "Lebanon's capital" , "Lebanese capital" , "Capital of 21 across" .)