Understanding the distribution of seagrass in the Great Barrier Reef (GBR) allows us to assess the interaction of risks, protections and seagrass species diversity. The GBR has large areas of seagrass habitat extending from intertidal waters to 76 metres below mean sea level. It includes 12-15 species although these are not evenly distributed in location and extent. There are approximately 13 major spatial management tools that can be used to protect or manage seagrass in this region. They range from marine park management zones with very high levels of protection (e.g. Preservation Zones) to locations where only extra care is required (e.g. RAMSAR sites). Management is complicated by several levels of government responsibility. Land based and intertidal management including port management is predominately in the domain of the Queensland State Government while most of the GBR is managed by the Commonwealth. The complex spatial management and the uneven distribution of seagrass habitat present both a problem and an opportunity. Improved modelling ability now enable us to categorize interactions and to identify the key areas for management intervention that best protect seagrass biodiversity. In this talk we take you through our approach and our direction for the future.