Atrazine is a herbicide widely used in the control of weeds in crops such as corn, sugar cane, and sorghum. It is often found in aquatic environments, where it can potentially endanger nontarget organisms such as microalgae. The present study evaluated atrazine toxicity to seven different species of Chlorophyceae and the tolerance of the species to the herbicide was related to morphological, photosynthetic, chlorophyll‐a content and the activity of the glutathione‐S‐transferase enzyme (GST). The comparison of median effect concentration (EC50) values for growth inhibition indicates higher toxicity of atrazine for Pseudopediastrum boryanum and Desmodesmus communis, intermediate toxicity for Ankistrodesmus densus, Chlamydomonas puliminiorfes, and Raphidocelis subcapitata, and lower toxicity for Kirchneriella lunaris and Ankistrodesmus falcatus (EC50: 38, 42, 66, 103, 248, 1004, and 1585 µg L−1 atrazine, respectively). Principal component analysis (PCA) with algal characteristics suggested that the atrazine‐sensitive algae P. boryanum and D. communis were positively associated with photosynthetic levels and negatively associated with GST activity and chlorophyll‐a concentration. The PCA also suggested that the atrazine‐tolerant algae A. falcatus and K. lunaris were positively associated with morphological parameters, where the larger the cell size, the more tolerant. Although it is difficult to associate a single characteristic of algae as the key factor determining the tolerance to atrazine, results presented in this work indicate that the cell area, the photosynthetic parameters (mainly saturating irradiance), chlorophyll‐a content, and the biotransformation by GST in combination may be potential predictors for the differential tolerance of Chlorophyceae species to the herbicide. Environ Toxicol Chem 2022;41:1675–1685. © 2022 SETAC