Colours seen in muddy estuary (4)
I believe the answer is:
dyes
'colours' is the definition.
(dyeing is a kind of colouring)
'in muddy estuary' is the wordplay.
'in' indicates the answer is hidden within the clue.
'DYES' is hidden in the letters of 'muddy estuary'.
'seen' acts as a link.
(Other definitions for dyes that I've seen before include "Colours (fabric)" , "Many a pigment" , "Colour" , "Stains" , "Substances for staining or colouring" .)