Stuckenia pectinata, a submerged macrophyte of eutrophic to hyper-eutrophic fresh to brackish waters, faces management and climatic-forced increment of salinity and irradiance in Vistonis Lake (Greece) that may endanger its existence and the ecosystem functioning. A pre-acclimated clone under low irradiance and salinity conditions was treated to understand the effects of high salinity and irradiance on a suite of subcellular (chlorophyll a fluorescence kinetics and JIP-test, and chlorophyll content) to organismal (relative growth rate—RGR) physiological parameters. The responses to high irradiance indicated the plant’s great photo-acclimation potential to regulate the number and size of the reaction centers and the photosynthetic electron transport chain by dissipation of the excess energy to heat. A statistically significant interaction (p < 0.01) of salinity and irradiance on Chl a, b content indicated acclimation potential through adjusting the Chl a, b contents. However, no significant (p > 0.05) difference was observed on Chl a/b ratio and the RGR, indicating the species’ potential to become acclimatized by reallocating resources to compensate for growth. Thus, the regulation of photosynthetic pigment content and photosystem II performance consisted of the primary growth strategy to present and future high salinity and irradiance stressful conditions due to eutrophication management and the ongoing climatic changes.