Aquatic plants naturally come into direct contact with microcystins in eutrophic water bodies suffering from cyanobacteria blooms. In the present study, the bioaccumulation and detoxification of microcystin-LR (MC-LR) in three submerged macrophytes, Ceratophyllum demersum L., Vallisneria natans (Lour.) Hara and Myriophyllum spicatum L., were investigated. Our results showed that the average daily uptake rates of C. demersum (3.85 μg kg⁻¹ dry weight (DW) d⁻¹) and M. spicatum (3.97 μg kg⁻¹ DW d⁻¹) were both significantly higher than that of V. natans (2.88 μg kg⁻¹ DW d⁻¹). The average daily biotransformation rates of MC-LR in C. demersum, V. natans and M. spicatum were 1.95, 2.16 μg kg⁻¹ DW d⁻¹ and 3.97 μg kg⁻¹ DW d⁻¹, which deceased to 0.75, 0.64 and 1.78 μg kg⁻¹ DW d⁻¹, respectively, after pre-treatment with buthionine sulfoximine (BSO, a specific and potent inhibitor of glutathione (GSH) biosynthesis). GSH content significantly decreased by 48.8%, 65.7% and 31.9% in C. demersum, V. natans and M. spicatum on days 8, compared to the controls. In addition, glutathione S-transferase (GST) activity and glutathione reductase (GR) activity of all three plants were stimulated by MC-LR during the whole bioaccumulation period. These results indicated that GSH was involved in the detoxication of MC-LR in plants. Moreover, results of malondialdehyde (MDA) content indicated that cell damage occurred in C. demersum, which could recover in the detoxification period; whereas the detoxification system could protect V. natans and M. spicatum from the toxicity of 5 μg L⁻¹ MC-LR.