Plant response to salt stress involves changes in intracellular ion concentrations that can be estimated by ion-selective fluorescent dyes. Conventional confocal/fluorescent imaging does not always accurately reflect the process, since it is dependent not only on the ion concentration but on the dye concentration itself. Fluorescent lifetime imaging (FLIM) can resolve this problem: images derived under this technique are based on the fluorescent lifetime distribution of the bound/unbound state of the fluorophore, and not on the fluorescent intensity. On the example of 2′-7′-bis(carboxyethyl)-5(6)-carboxyfluorescein (BCECF) and Ca Green, we demonstrate the potential of FLIM technique in salinity studies.