Home Counties harbours smell cleaner (6)
I believe the answer is:
sponge
'cleaner' is the definition.
'home counties harbours smell' is the wordplay.
'home counties' becomes 'se' (Home Counties in the South East of England).
'harbours' indicates putting letters inside.
'smell' becomes 'pong' (pong can informally mean a bad smell).
'se' enclosing 'pong' is 'SPONGE'.
(Other definitions for sponge that I've seen before include "Aquatic creature; cake" , "Piece of porous rubber" , "Scrounge; wiper" , "marine life?" , "Cadge; type of cake" .)