Seagrass meadows, including those formed by Zostera noltei, play a crucial role in marine ecosystem health by providing habitat stability and coastal protection. In the Romanian Black Sea, Z. noltei meadows are critically endangered due to pressures from eutrophication, habitat loss, and climate change. This study presents a comprehensive baseline assessment of Z. noltei meadows near Mangalia, Romania, utilizing in situ field methods and UAV mapping conducted in the spring and summer of 2023. Seven meadow sites (Z1–Z7) were identified, with notable variability in density, shoot counts, and coverage across sites. Site Z1 exhibited the highest density (1223 shoots/m⁻²) and Z5 and Z7 the longest leaves (an average of 60 cm), reflecting possible environmental influences. Statistical analyses revealed significant inter-site differences in shoot density and leaf length, with density emerging as a primary differentiator. Ex situ analyses of epiphyte load indicated a median, balanced epiphyte load. This baseline dataset supported the selection of Z1 as a reference donor site for seagrass relocation activities along the Romanian coast in 2023. By providing critical insights into Z. noltei structure and health, this study supports future conservation efforts and evidence-based management of these vulnerable coastal habitats.