The release of cyanobacterial toxins during algal bloom has adverse effects on aquatic plants and animals. This study aimed to understand the toxic effects and mechanism of microcystin-LR (MC-LR) on the seedling growth and physiological responses of Iris pseudacorus L. (calamus). After a one-month exposure experiment, the growth and development of the calamus leaves were significantly inhibited, and this inhibitory effect was verified to be concentration dependent. Furthermore, the cell membrane system was damaged, and the photosynthesis was also adversely affected by MC-LR. The relative conductivity of the leaves increased from 10.96% to 97.51%, and the total chlorophyll content decreased from 0.89 mg/g to 0.09 mg/g. Notably, the behavior of the roots in the presence of MC-LR was different from that of the leaves. The seedlings needed to absorb more nutrients to maintain the normal growth at low-toxin concentrations, but the high concentration of (over 250 μg/L) MC-LR exceeded the tolerance of plants and inhibited the growth of roots. In addition, MC-LR led to an excessive accumulation of H₂O₂, and the seedlings enhanced the activities of catalase, peroxidase, and superoxide dismutase to resist oxidative stress. The presence of MC-LR also affected the capacity of the plants to absorb nitrogen and phosphorus. The removal efficiency of NO₃⁻-N, the main source of nitrogen, was 63.53% in the presence of 100 μg/L MC-LR. As a result, the pH increased, and the growth of plants was indirectly inhibited. Therefore, the presence of MC-LR could affect the purification efficiency of calamus in eutrophic water. This study provides theoretical support for the selection of plants in the eutrophic water.