Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
Green and stinking from what?
Algae? Try soaking it in hydrogen peroxide. 3% concentration is fine, or if you have a stronger solution, dilute it. You could soak it in bleach. Not at the same time.
Is it the rock itself that is green? Like some sort of chemical reaction?
You can scrub rocks with something stiffer than a toothbrush. Perhaps a really stiff plastic brush?
If you want to try a wire brush then test somewhere that will be hidden. The wire might scratch the rock.
I do not think it is possible to separate those materials. A possibility: Buy new soil, but not very much. Put the mixed materials lower in the tank, and put just enough of the clean stuff on top to hide the blended materials.