Aquatic plants are potentially impacted by microcystins (MCs) in lakes experiencing harmful algal blooms. However, how these plants respond, and possibly adapt to osmotic stress caused by MCs is unclear. Vallisneria natans is a pioneer taxon with a global distribution in eutrophic lakes. In this study, we investigated the effect of MC-LR on morphological structure, water retention, osmoregulatory ability, and homeostasis of calcium (Ca2+) and potassium (K+) ions in V. natans leaves. Results showed that the morphological changes caused by MC-LR included increased volumes of epidermal and mesophyll cells, changes in their lignification level, and the degradation of chloroplast structure and dissolution of starch granules. The increased moisture content and water potential with MC-LR concentration were consistent with the occurrence of osmotic stress, and the decreased osmotic potential implied the activation of osmoregulation. Soluble sugar and free amino acid concentrations increased at MC-LR treatments ≥10 μg/L, while inorganic ion K+ content increased in all MC-LR treatments. Although instantaneous K+inflow and Ca2+outflow occurred at 10 μg/L and 100 μg/L MC-LR, respectively, ≥1 μg/L MC-LR resulted in continuous K+ inflow and Ca2+ outflow within 24 h. Moreover, plasma membrane hyperpolarization was caused by MC-LR, especially at 1 and 10 μg/L. We suggest that Ca2+ efflux served as a signal molecule from the cytoplasmic matrix via Ca2+-ATPase, and the uptake of K+ was activated passively through transporters in response to MC-LR-induced plasma membrane hyperpolarization. Therefore, the uptake of K+ was a part of the response but not an adaptation to MC-LR stress, and is considered the cause for the uptake of water in leaves. Ca2+ and K+ homeostasis of V. natans leaves was disrupted by MC-LR concentrations as low as 1 μg/L, suggesting that aquatic plants in most eutrophic lakes may experience negative impacts such as Ca2+ loss, impacts to cell water balance, and alteration in cellular morphology, due to osmotic stress caused by MC-LR.