Small aquatic bird in rear of vessel (5)
I believe the answer is:
stern
'rear of vessel' is the definition.
'small aquatic bird' is the wordplay.
'small' becomes 's' (abbreviation - e.g. clothes size).
'aquatic bird' becomes 'tern' (tern is a kind of aquatic bird).
's'+'tern'='STERN'
'in' acts as a link.
(Other definitions for stern that I've seen before include "Severe in the rear of the ship?" , "Harsh at the back of the ship" , "Tail of a beagle" , "enforcing submission" , "Grave; rear" .)