This paper describes seagrass species and percentage cover point-based field data sets derived from georeferenced photo transects. Annually or biannually over a ten year period (2004-2014) data sets were collected using 30-50 transects, 500-800 m in length distributed across a 142 km(2) shallow, clear water seagrass habitat, the Eastern Banks, Moreton Bay, Australia. Each of the eight data sets include seagrass property information derived from approximately 3000 georeferenced, downward looking photographs captured at 2-4 m intervals along the transects. Photographs were manually interpreted to estimate seagrass species composition and percentage cover (Coral Point Count excel; CPCe). Understanding seagrass biology, ecology and dynamics for scientific and management purposes requires point-based data on species composition and cover. This data set, and the methods used to derive it are a globally unique example for seagrass ecological applications. It provides the basis for multiple further studies at this site, regional to global comparative studies, and, for the design of similar monitoring programs elsewhere.