Nautical position affects deserted seabird (6)
I believe the answer is:
astern
'nautical position' is the definition.
(I've seen this in another clue)
'affects deserted seabird' is the wordplay.
'deserted' means to remove the middle letters.
'seabird' becomes 'tern' (tern is a kind of seabird).
'affects' with its middle removed is 'as'.
'as'+'tern'='ASTERN'
(Other definitions for astern that I've seen before include "at the vessel's rear" , "Towards back of boat" , "back for sailors" , "Ran set (anag.)" , "Toward the back of a boat" .)