Replace one sort of vessel (3)
I believe the answer is:
sub
This clue is a double definition.
'replace' is the first definition.
(substitute)
'one sort of vessel' is the second definition.
(submarine)
(Other definitions for sub that I've seen before include "Underwater vessel" , "Briefly, membership fee or stand-in" , "Contribution; a boat" , "Prefix denoting under" , "Type of sandwich" .)