Seagrasses have adapted to a submerged lifestyle in seawater through a complex set of evolutionary processes. However, they show sensitivity to increases in natural salinity levels such as those commonly found in discharges of desalination plants, which have exponentially grown due to water scarcity in highly populated temperate areas, such as the Mediterranean basin. This study assessed the effects of brine-derived hypersalinity on the Mediterranean seagrass Posidonia oceanica, focusing on the metabolic responses of shoot apical meristems (SAMs). Although most physiological and genetic studies have used leaves, SAMs are more directly correlated with plant survival and might be more responsive to salinity stress. The experiments were: a controlled mesocosm of more than six practical salinity units (psu) over natural levels using either artificial salts or desalination brine and field transplantation experiments comparing two sites following the dilution plume of the brine (+5 and + 2 psu) with control. Hydrogen peroxide (H2O2), thiobarbituric acid reactive substances (TBARS), and ascorbate were measured to determine oxidative stress and damage, as well as relative expression of genes related to osmotic regulation and oxidative responses. Overall, relative expression of genes related to osmotic regulation (SOS1, SOS3, AKT 2/3) and oxidative stress (STRK1, CAT, MnSOD, FeSOD, APX, GR) was higher in SAMs at higher brine exposures, indicating a more active metabolic response in this organ. Similarly, reactive oxygen species (ROS) production and lipid peroxidation were higher closer to brine discharge and total ascorbate lower, indicating a correlative response with stressor intensity. These findings confirm that SAMs play an essential role in P. oceanica hypersalinity responses and its adaptation to life in the marine environment. Finally, the use of P. oceanica SAMs in this study is highly recommended for an early detection of threats caused by desalination brines that may cause physiological damage and meadow regression.