Estuary, except the mouth, is brown (5)
I believe the answer is:
umber
'brown' is the definition.
(umber is a kind of brown)
'estuary except the mouth' is the wordplay.
'estuary' becomes 'humber' (The Humber is an estuary).
'except the mouth' means to remove the first letter (mouth can mean an opening or entrance).
'humber' with its first letter removed is 'UMBER'.
'is' is the link.
(Other definitions for umber that I've seen before include "Natural colouring matter, dark brown" , "Brown earthy mineral" , "Brownish pigment" , "Earthy colour" , "Brown earthy substance used as pigment" .)