Two ducks crossing harbour in European city (6)
I believe the answer is:
oporto
'european city' is the definition.
(city in Portugal)
'two ducks crossing harbour' is the wordplay.
'two ducks' becomes 'oo'.
'crossing' means one lot of letters goes inside another.
'harbour' becomes 'port' (I've seen this before).
'oo' placed around 'port' is 'OPORTO'.
'in' acts as a link.
(Other definitions for oporto that I've seen before include "Portuguese wine trade centre" , "Portugal's second city" , "Iberian location" , "City near the mouth of the River Douro" , "Iberian city" .)