Microalgae are biological indicators of heavy metal pollution. Cadmium (Cd) and lead (Pb) are extremely toxic metals to aquatic organisms. In the present study, single and combined toxicity of Cd²⁺ and Pb²⁺ to Scenedesmus acutus and Schroederia sp. collected from the famous Xin’an River (Huangshan City) were evaluated. Treatments with 0.5-2.0 mg/L Cd²⁺ significantly reduced S. acutus population growth, and treatment with 2.0 mg/L Cd²⁺ significantly decreased Schroederia sp. population growth rate, suggesting a higher tolerance of Schroederia sp. than S. acutus to Cd²⁺ pollution. In addition, Cd²⁺ treatments significantly decreased chlorophyll a, carotene contents, and photosynthetic fluorescent parameters rETR_max and I_k, demonstrating that the harms on photosynthesis might be the underlying mechanism of Cd²⁺ toxicity to algae. Treatments with 5.0-15.0 mg/L Pb²⁺ did not significantly affected population growth and photosynthetic pigment content. However, combined exposure to Cd²⁺ and Pb²⁺ revealed antagonistic effects on both species. Overall, these results provide basic information to the ecological risk assessments of heavy metal pollution in the Xin’an River Basin.