Weed remains in fertiliser (6)
I believe the answer is:
potash
'fertiliser' is the definition.
(I know that potash is a type of fertiliser)
'weed remains' is the wordplay.
'weed' becomes 'pot' (synonyms).
'remains' becomes 'ash' (remains of a fire).
'pot'+'ash'='POTASH'
'in' is the link.
(Other definitions for potash that I've seen before include "Potassium compound used in agriculture and industry" , "Strong alkali derived from burnt wood" , "Alkali used as fertiliser" , "Agricultural chemical" , "The strange pathos of a potassium compound" .)