Ship on water only held by chain across harbour (6)
I believe the answer is:
bottom
'ship' is the definition.
(bottom is a kind of ship)
'on water only held by chain across harbour' is the wordplay.
I cannot really understand how this works, but
'on' could be 'to' and 'to' is found within the answer.
This may be the basis of the clue (or it may be nonsense).
(Other definitions for bottom that I've seen before include "Low point" , "Lowest of the low" , "cargo vessel?" , "Base; Shakespearean character" , "Lowest position" .)