This paper describes a lab-scaled experiment in which ethyl acetate of aqueous extract from Elodea nuttallii, species of submerged macrophytes, is analyzed by GC-MS and the allelopathic effect of ethyl acetate fraction on Microcystin aeruginosa is investigated. A total of 23 organic acids are identified and there is evidence that ethyl acetate fraction plays an active role in inhibiting growth of M. Aeruginosa. It is considered that the result could be useful in alleviation of waters eutrophication.