Photosynthetic apparatus analysis provides information about the physiological state of plants. Changes analyzed by the pulsed chlorophyll-fluorometer allow determining plant cells' metabolites' modifications even at inconsequential cellular damage. It was assessed the possible impact of various salinity levels: 0.584, 1.461, 2.922, and 5.844 PSU (Practical Salinity Unit) on the fluorescent characteristics of the pigment complexes of photosynthetic apparatus on the alien invasive waterweed species (Elodea canadensis (Michx., 1803)) of the most serious concern in Europe. The information about aquatic macrophyte photosynthetic systems: PSI and PSII was obtained. The results indicate that a high salinity level: 2.922 and 5.844 PSU, after a prolonged time of impact, seriously affect photosynthetic apparatus inhibition. The decrease in ∆F_v/F_m΄ values at 2.922 and 5.844 PSU indicates deterioration in macrophytes' physiological state in general. In the post-stress period, photosynthesis intensified. The interesting feature was noted, that a small water salinity level (0.584) stimulates the chlorophyll formation and increases the F_vF_m index.The research revealed the dependence of photosynthesis processes in plants on salinity levels. A rapid increase in the sensitivity of the PS II system of submerged macrophytes to high salinity was detected, which probably is related to the inhibition of protein synthesis. This data provides information for the further bio-diagnostics of the plant's overall condition and prediction of the exposure degree and the possibility of developing forecasts of growth and invasive plant distribution.