Better protected by largely safe, deep natural harbour (5,4)
I believe the answer is:
scapa flow
'natural harbour' is the definition.
'scapa flow' can be an answer for 'harbour' (I've seen this before). I'm not certain of the 'natural' bit.
'better protected by largely safe deep' is the wordplay.
'better' becomes 'cap' (both can mean to beat somebody else's attempt).
'protected by' indicates putting letters inside (inserted letters are held or protected).
'largely' means to remove the last letter (most but not all of the letters).
'deep' becomes 'low' (similar in meaning).
'safe' with its final letter taken off is 'saf'.
'cap' put into 'saf' is 'scapaf'.
'scapaf'+'low'='SCAPA FLOW'
Can you help me to learn more?
(Other definitions for scapa flow that I've seen before include "harbour" , "Wartime naval base in Orkney" , "Former naval base in the Orkney Islands" , "Landlocked anchorage in the Orkney Islands" .)