Seagrasses are habitat-forming species that support biodiversity and a wide range of associated ecosystem services, from blue carbon capture to providing nursery areas for a variety of organisms. Their decline has been documented worldwide and is attributed to human impacts ranging from habitat loss and eutrophication to the effects of climate change. However, recent recovery trends have also been documented due to reductions in stressors, passive and active restoration, and even changes in environmental conditions owing to local management. In this study, we document for the first time the occurrence of Zostera noltei in the downstream area of the River Minho Estuary. This occurrence was unexpected given the hydrological conditions of the estuary, characterised by dredging and siltation. We reconstructed the occurrence and historical distribution of seagrass beds, and showed that they have existed in the region for more than a decade. The current distribution area was mapped using high-resolution multispectral remote sensing techniques, and in situ photoquadrats to complement the remote sensing information with an evaluation of the seagrass cover. A current seagrass area of 0.81 ha was found with an average cover of 70%. However, the Minho Estuary continues to be strongly affected by sediment deposition, which may affect the seagrass population in the long term. Continued surveys are recommended to confirm the long-term trend of colonisation of this important habitat, which ultimately provides so many benefits to coastal ecosystems and humankind.