Boat seen after short time in capital (6)
I believe the answer is:
moscow
'capital' is the definition.
(capital of Russia)
'boat seen after short time' is the wordplay.
'boat' becomes 'scow' (scow is a kind of boat).
'seen after' is a charade indicator (letters next to each other).
'short time' becomes 'mo' (as in 'just a mo').
'scow' put after 'mo' is 'MOSCOW'.
'in' acts as a link.
(Other definitions for moscow that I've seen before include "capital city" , "Kremlin location" , "Olympic city, 1980" , "City of 13" , "Russian city" .)