This dataset describes the spatial distribution of the seagrass meadows of Zostera noltei, restricted to intertidal areas, in Ria de Aveiro coastal lagoon (Portugal) in 2014. Ria de Aveiro is a Long-Term Ecological Research (LTER) site (http://www.lter-europe.net/) with several important habitats that justify its inclusion in the Natura 2000 network and classification as a Special Protection Area, comprising areas classified as Sites of Community Importance. Zostera noltei (Hornemann, 1832) meadows are important habitats and nursery areas for many species, contributing to increase biodiversity, and relevant as Blue C reservoirs in Ria de Aveiro, supporting climate regulation and improving ecosystem health. However, Zostera noltei may be threatened due to changes in the lagoon hydrodynamics, since sediment remobilization negatively affects the seagrass stability, due to global changes and other drivers. This dataset allows locating the spatial distribution and extent of Zostera noltei. Using an Unmanned Aerial Vehicle (UAV, drone), aerial photographs were obtained and, through Geographical Information System (GIS) procedures and ground-truth validation, the seagrass spatial distribution at Ria de Aveiro was assessed. With this information, the authorities can establish a security perimeter when human interventions and activities like dredging, which endanger the seagrass stability and conservation status, are foreseen.