Phytoremediation of manganese (Mn)-contaminated water requires the selection of Mn-tolerant species. This study reports on physiological changes and Mn bioaccumulation in the aquatic macrophyte Pistia stratiotes cultivated under various MnCl2 concentrations: control, 80, 340, 600, 1000, 2000, and 4000 µM. Few visual symptoms of Mn toxicity, such as chlorosis, were observed after 10 days, especially in plants treated with 2000 and 4000 µM MnCl2. High Mn accumulation was recorded, with maximum values of 23,700 and 24,600 µg g−1 DW in the shoots and roots, respectively, at 4000 µM Mn, contrasting with 825.01 and 1587.53 µg g−1 DW in control plants. Cellular fractioning showed that Mn in shoots and roots was mainly associated with the cell wall, with approximately 90% of the Mn in roots detected in the apoplast. There were no significant changes in net CO2 assimilation or respiratory rates after 5 and 10 days of Mn exposure. These results demonstrate that P. stratiotes is a Mn hyperaccumulator species with excellent phytoremediation potential, as shown by its high bioaccumulation capacity and its ability to maintain photosynthetic efficiency under Mn stress.