Port for mother after morning rest perhaps (9)
I believe the answer is:
amsterdam
'port' is the definition.
(I know that Amsterdam is a port)
'mother after morning rest perhaps' is the wordplay.
'mother' becomes 'dam' (female parent of an animal).
'after' means one lot of letters go next to another.
'morning' becomes 'am' (as in 12:00 AM).
'perhaps' indicates an anagram.
'rest' with letters rearranged gives 'ster'.
'am'+'ster'='amster'
'dam' after 'amster' is 'AMSTERDAM'.
'for' acts as a link.
(Other definitions for amsterdam that I've seen before include "European capital" , "9/11 [OLYMPIC VENUE]" , "city with many canals" , "Dutch city of canals" , "Western European city, a major diamond centre" .)