Hell no, you can't.
Is it mold or algae? If it is algae growing on the surface of your medium, they sell stuff for that and caps to keep the medium covered and prevent light from reaching your medium (they might not exactly be compatible with what you're doing). Algae needs light to grow, mold doesn't. Hydrogen peroxide will kill algae and mold and prevent the growth of other microbes. You might consider adding a tablespoon or so. It breaks down into water and oxygen, both of which the roots utilize. It just cannot be used in conjunction with any beneficial bacteria or mycorrhizal fungi. Beneficials such as those could probably also be used to treat or prevent whatever microbiological issue you're having; mold spores are ubiquitous and it is easy for any kind of microbe to take hold when there isn't any competition.