Cu²⁺ and Hg²⁺ are two typical contaminants. Previous studies on toxicity of Cu²⁺ and Hg²⁺ to green algae mainly employed concentrations higher than environmental levels. Since the results varied among different strains of the same species, toxicity assessment using local green alga strains might be more accurate for revealing risks of Hg²⁺ and Cu²⁺ to local environments. In the present study, Scenedesmus quadricauda and Scenedesmus acutus were isolated from the Xin’an River in Huangshan City, China. Both were treated with 0.01-0.15 mg/L Hg²⁺ or 0.5-10 mg/L Cu²⁺. The results showed that Hg²⁺ and Cu²⁺ were highly toxic. Treatment with 0.1 mg/L Hg²⁺ completely inhibited growth of S. acutus and 0.15 mg/L Hg²⁺ inhibited growth of S. acutus, but no significant changes were observed in contents of photosynthetic pigments and chlorophyll fluorescence parameters, suggesting that toxicity of Hg²⁺ might not be due to inhibition on photosynthesis. Treatments with 0.5 mg/L Cu²⁺ depressed cell growth, and higher levels of Cu²⁺ decreased contents of photosynthetic pigments (chl-a, car or chl-b) in S. quadricauda and S. acutus. Moreover, S. quadricauda might be more sensitive to heavy metal treatments than S. acutus. These results should be useful for evaluating environmental risks of Hg²⁺ and Cu²⁺ to Huangshan City.