The behaviour and spatial use patterns of juvenile manta rays within their critical nursery habitats remain largely undocumented. Here, we report on the horizontal movements and residency of juvenile reef manta rays (Mobula alfredi) at a recently discovered nursery site in the Wayag lagoon, Raja Ampat, Indonesia. Using a multi-disciplinary approach, we provide further corroborative evidence that the lagoon serves as an important M. alfredi nursery.