Prymnesium parvum is a harmful alga found in brackish waters worldwide whose toxins can be lethal to aquatic organisms. Established field methods to control blooms of this species, however, are unavailable. Earlier studies showed that various extracts of giant reed (Arundo donax) can suppress P. parvum growth and that ellipticine, an allelochemical present in giant reed, is a potent algicide against this species. The unintended effects of giant reed products on nontarget organisms, however, are not fully understood. This study determined the effects of giant reed leachate (aqueous extract of dried chips) and ellipticine on growth of P. parvum and the green microalga Chlorella sorokiniana; survival and reproduction of the planktonic crustacean Daphnia pulex; and hatching success, larval survival, and larval swimming behavior of the teleost fish Danio rerio. Leachate made with 3 g chips L⁻¹ was lethally toxic to P. parvum and D. pulex, stimulated C. sorokiniana growth, and impaired D. rerio behavior. Leachate at 1 g L⁻¹ fully suppressed P. parvum growth, had moderate effects on D. pulex reproductive output, and had no effects on D. rerio. Ellipticine at 0.01 mg L⁻¹ irreversibly inhibited P. parvum growth, acutely but reversibly inhibited C. sorokiniana growth, slightly delayed D. pulex reproduction, and had no effects on D. rerio. These observations suggest that when applied at appropriate concentrations, natural products derived from giant reed can be used as tools to specifically control P. parvum growth with minimal effects on nontarget species.