Bisphenol A and its structural congeners are increasingly recognized as emerging contaminants with toxic and estrogenic potential that have been widely used in many consumer products. Due to their widespread occurrence in aquatic environment, they could pose risks to the primary producers, such as microalgae. Therefore, the objective of this study was to examine the toxicity of bisphenol A, its six structural congeners, and their mixture towards the green algae Chlorella vulgaris and Desmodesmus armatus. Bisphenol A (average 14 days, EC50: 42.29 mg L−1) exhibited less harmful effect than structural congeners, such as bisphenol AF, bisphenol G, bisphenol X for C. vulgaris (average 14 days, EC50: 22.39 mg L−1) and bisphenol AF, bisphenol G, bisphenol M, bisphenol X for D. armatus (average 14 days, EC50: 27.16 mg L−1), respectively. Moreover, exposure to combined bisphenol A and its structural congeners leads to synergistic effects. Thus, the increased adverse effect caused by complex chemical mixture poses a greater risk to microalgae. The order of toxic effect (14 days, EC50) of individual and combined structural congeners was: bisphenol G > bisphenol X > mixture > bisphenol AF > bisphenol A > bisphenol Y > bisphenol M > bisphenol P for C. vulgaris and mixture > bisphenol G > bisphenol X > bisphenol M > bisphenol AF > bisphenol A > bisphenol Y > bisphenol P for D. armatus, respectively. This is the first time that the toxicity of structural congeners of bisphenol A and its mixture to microalgae is described. Furthermore, these results were conducted to assess potential ecological risk of these compounds in the aquatic environment.