In the Mediterranean, anthropogenic pressures (specifically those involving nutrient loads) have been progressively moved to deeper off-shore areas to meet current policies dealing with the protection of marine biodiversity (e.g., European Directives). However, conservation efforts devoted to protecting Posidonia oceanica and other vulnerable marine habitats against anthropogenic pressures have dedicated very little attention to the deepest areas of these habitats. We studied the remote influence of off-shore nutrient discharge on the physiology and structure of deep P. oceanica meadows located nearest to an urban sewage outfall (WW; 1 km) and an aquaculture facility (FF; 2.5 km). Light reduction and elevated external nutrient availability (as indicated by high δ15N, total N and P content and N uptake rates of seagrass tissues) were consistent with physiological responses to light and nutrient stress. This was particularly evident in the sites located up to 2.5 km from the WW source, where carbon budget imbalances and structural alterations were more evident. These results provide evidence that anthropogenic nutrient inputs can surpass critical thresholds for the species, even in off-shore waters at distances within the km scale. Therefore, the critical distances between this priority habitat and nutrient discharge points have been underestimated and should be corrected to achieve a good conservation status.