Previous studies reported anatoxin-a (ANTX-a) accumulation and bioremediation by the aquatic macrophyte Lemna trisulca. In the present study, we determined that cultivation of this macrophyte in medium containing ANTX-a at a concentration similar to that occur in nature (1.0μg·mL−1) did not cause any changes in the plant physiology. A much higher toxin concentration (12.5μg·mL−1) reduced photosynthetic efficiency by 27% compared with the control, but had no significant effect on the respiration process. L. trisulca cultivated in medium containing 25.0μg of ANTX-a·mL−1 reduced the chla content by 40% on the 18th day of the experiment, the chlb content by 35% on the 14th day of the experiment and the total carotenoids by 11% on the 24th day of the experiment. ANTX-a at concentrations ≤12.5μg·mL−1 did not cause any significant differences in the concentration of released anions (Cl−, NO3− and SO42−) compared to the control. However, cultivation of L. trisulca with 5μg of ANTX-a·mL−1 resulted in a 1.8-fold increase in the concentration of K+ released into the medium compared with the control. The amount of Na+, Ca2+ and Mg2+ released after plant exposure to 12.5μg of ANTX-a·mL−1 was 1.3-fold, 1.6-fold and 1.7-fold higher, respectively, compared to the control. ANTX-a had a slight effect on the protein content and the oxidoreductase activity in the macrophyte. After 24h, there were no significant differences in the enzymatic activity of the superoxide dismutase, catalase, ascorbate peroxidase, glutathione peroxidase and glutathione reductase, regardless of the ANTX-a concentrations in the media. Only polyphenol oxidase showed a slight increase in the activity in media containing ANTX-a. These findings confirmed that L. trisulca has a high tolerance to this toxin and a great potential as a phytoremediation agent in the aquatic environments.