Colour of muddy estuary (3)
I believe the answer is:
dye
'colour' is the definition.
(dyeing is a kind of colouring)
'of muddy estuary' is the wordplay.
'of' indicates the answer is hidden within the clue.
'DYE' can be found hidden inside 'muddy estuary'.
(Other definitions for dye that I've seen before include "Colouring agent" , "Colouring liquid" , "Colouring matter" , "Colouring material" , "Colourant" .)