The development of science and technology and industry has brought about severe pollution to water environment. Research advances in the ecotoxicological effects of heavy metals, organic compounds and nano-materials on algae are reviewed from aspects of the growth, enzyme activity, photosynthesis, cell structure and metabolism of algae. Furthermore, suggestions and prospects for researches in this area are put forward in the hope of laying foundation for the selection of sensitive algae species and the basic research of ecotoxicology.