Increasing threats to natural ecosystems from local and global stressors are reinforcing the need for baseline data on the distribution and abundance of organisms. We quantified spatial and/or temporal patterns of seagrass distribution, shoot density, leaf area index, biomass, productivity, and sediment carbon content in shallow water (0–5 m) at Lizard Island, Great Barrier Reef, Australia, in field surveys conducted in December 2011 and October 2012. Seagrass meadows were mapped using satellite imagery and field validation. A total of 18.3 ha of seagrass, composed primarily of Thalassia hemprichii and Halodule uninervis, was mapped in shallow water. This was 46% less than the area of seagrass in the same region reported in 1995, although variations in mapping methods may have influenced the magnitude of change detected. There was inter-annual variability in shoot density and length, with values for both higher in 2011 than in 2012. Seagrass properties and sediment carbon content were representative of shallow-water seagrass meadows on a mid-shelf Great Barrier Reef island. The data can be used to evaluate change, to parameterize models of the impact of anthropogenic or environmental variability on seagrass distribution and abundance, and to assess the success of management actions.