Earthy pigment in mineral aggregate contains carbon and hydrogen (5)
I believe the answer is:
ochre
'earthy pigment' is the definition.
(I've seen this before)
'mineral aggregate contains carbon and hydrogen' is the wordplay.
'mineral aggregate' becomes 'ore' (I've seen this before).
'contains' means one lot of letters goes inside another.
'carbon' becomes 'c' (C is the chemical symbol for carbon).
'and' means one lot of letters go next to another.
'hydrogen' becomes 'H' (chemical symbol).
'c'+'h'='ch'
'ore' enclosing 'ch' is 'OCHRE'.
'in' acts as a link.
(Other definitions for ochre that I've seen before include "Yellow-orange hue" , "Yellow-orange colour" , "Earth used in pigments" , "What gives a yellow colour" , "natural colouring" .)