Deep trench lacking a facility for craft (6)
I believe the answer is:
marina
'facility for craft' is the definition.
(I know this)
I cannot understand how the rest of the clue works.
(Other definitions for marina that I've seen before include "Airman (anag)" , "Yacht station" , "seaside area" , "where yachts moor" , "Base for pleasure boats" .)