Deepest of three originally in port (9)
I believe the answer is:
lowestoft
'port' is the definition.
(I've seen this before)
'deepest of three originally' is the wordplay.
'deepest' becomes 'lowest' ('low' can be similar in meaning to 'deep').
'originally' indicates taking the first letters.
The first letter of 'three' is 't'.
'lowest'+'of'+'t'='LOWESTOFT'
'in' is the link.
(Other definitions for lowestoft that I've seen before include "Suffolk resort" , "Suffolk town" , "fishing port" .)