Recent reports tend to predict the increase of harmful cyanobacteria in water systems worldwide due to the climatic and environmental changes, which would compromise water quality and public health. Among abiotic changes, the higher salinities are expected to promote the growth of some harmful species such as Planktothrix agardhii, which is known to build up blooms in brackish areas. Since P. agardhii is a common cyanotoxin producer (microcystin-producing), we investigated here the growth and tolerance of this species when exposed in vitro to a range of salinity levels, while assessing its microcystins variation and production in batch cultures during a time-frame experiment of 18 days. The study revealed a salt acclimation of the brackish P. agardhii that still produced microcystins in salty cultures while maintaining its growth ability in low to medium salinities (ranged from 0 to 7.5 g L−1). For higher salinity concentrations (10 to 12.5 g L−1), microcystins were still detected, while significantly lower growth rates were obtained during the exponential growth phase. This suggests that moderate to high salt ranges do not inhibit the microcystins production of P. agardhii at least for several weeks. Finally, the predicted remediation perspectives in a context of environment salinization assumed by environmental policies may be insufficient to eradicate this potential toxic cyanobacteria, especially when this species is already dominant in the waterbodies.