The Mediterranean endemic seagrass Posidonia oceanica is generally regarded as a stenohaline species, highly sensitive to salinity increments; however, in a few particular cases, natural populations can grow under salinity levels above its normal threshold of tolerance. One such case is a population of P. oceanica in the southeastern coastal region of Spain, which is able to survive under the fluctuating influence of hypersaline waters coming from an adjacent coastal lagoon (Mar Menor). The present work examines the physiological mechanisms underlying the species' ability to overcome this hypersaline stress and persist in the long term. To this end, the physiological, morphological, and population statuses of plants from the site of influence were compared to those from a reference site where plants grew under normal conditions. P. oceanica leaves from the influenced sites showed more negative water potentials than those from the reference sites as a response to maintain a positive water balance under hypersaline conditions. However, these lower water potentials were not explained by the accumulation of intracellular solutes since their osmotic potential were similar to reference leaves and their ionic content generally lower. In addition, these leaves also accumulated higher concentrations of proline and soluble sugars but these organic osmolytes are more likely acting as osmo-protectants, rather than as osmoticums. These responses indicated that plants growing at the influenced site have developed physiological strategies to maintain lower ion concentration in their leaf tissues in order to avoid the alteration of ion homeostasis (i.e., ionic ratios), which can be toxic for plant metabolism. Photosynthesis and photochemistry were not adversely affected in leaves exposed to hypersalinity; in fact, these processes showed a tendency to become enhanced, possibly to support the assimilation of anthropogenic nitrogen coming from the lagoon waters. At the individual and population levels, P. oceanica plants growing under the influence of hypersaline waters exhibited a marked reduction in shoot size compared to those at the reference site, while shoot density and population growth rates were similar to those of the reference site and remained stable over time. This shoot size reduction involves a lower demand of metabolic resources necessary to maintain vegetative structures, which is mainly required for metabolic adjustments at the physiological level. We propose that this morphological adaptation serves as a stress-coping mechanism, helping the species to inhabit this unfavorable environment, as has been widely described for terrestrial plants subjected to long-term environmental stress.