Effects of various concentrations of Cu2+ and Zn2+ (0.0, 0.1, 0.25, 0.5, or 1.0 mg/L) on the growth, malondialdehyde (MDA), the intracellular calcium, and physiological characteristics of green algae, Cladophora, were investigated. Low Zn2+ concentrations accelerated the growth of Cladophora, whereas Zn2+ concentration increases to 0.25 mg/L inhibited its growth. Cu2+ greatly influences Cladophora growth. The photosynthesis of Cladophora decreased under Zn2+ and Cu2+ stress. Cu2+ and Zn2+ treatment affected the content of total soluble sugar in Cladophora and has small increases in its protein content. Zn2+ induced the intracellular calcium release, and copper induced the intracellular calcium increases in Cladophora. Exposure to Cu2+ and Zn2+ induces MDA in Cladophora. The stress concent of Cu2+ was strictly correlated with the total soluble sugar content, Chla+Chlb, and MDA in Cladophora, and the stress concent of Zn2+ was strictly correlated with the relative growth rate (RGR) and MDA of Cladophora.