European port in effect up over choppy seas (6)
I believe the answer is:
odessa
'european port' is the definition.
(Ukrainian port)
'effect up over choppy seas' is the wordplay.
'effect' becomes 'do' (synonyms).
'up' says the letters should be written backwards (in down clue: letters go upwards).
'over' means one lot of letters go next to another.
'choppy' is an anagram indicator (choppy implies disruption).
'do' back-to-front is 'od'.
'seas' with letters rearranged gives 'essa'.
'od'+'essa'='ODESSA'
'in' is the link.
(Other definitions for odessa that I've seen before include "Do seas come into Ukrainian city?" , "Ukrainian location" , "Seaport" , "Black Sea location" , "Battleship Potemkin mutiny port" .)