A two species non-autonomous competitive phytoplankton system with Beddington-DeAngelis functional response and the effect of toxic substances is proposed and studied in this paper. Sufficient conditions which guarantee the extinction of a species and global attractivity of the other one are obtained. The results obtained here generalize the main results of Li and Chen [Extinction in two dimensional nonautonomous Lotka-Volterra systems with the effect of toxic substances, Appl. Math. Comput. 182(2006)684-690]. Numeric simulations are carried out to show the feasibility of our results.