Aldabra Atoll occupies a unique place among the world's atolls due to the wealth of biodiversity it supports, its relatively undisturbed status and its designation as a World Heritage Site. This landmark conservation designation was due largely to the scientific advocacy and campaigning work of David Stoddart, with its strong focus on creating detailed and accurate inventories of the biological and physical attributes of this remote atoll. The lagoon mapping campaign described in the present study continues this tradition, making use of recent developments in geospatial technology to provide a detailed snapshot of the large and shallow lagoon that has hitherto been unavailable to physical and ecological science. Here we provide the first detailed maps of benthic community character and bathymetry in the Aldabra lagoon, the output of two related mapping exercises undertaken in February 2009 as part of a collaborative project between Cambridge Coastal Research Unit and the Seychelles Islands Foundation. The lagoon environment of Aldabra Atoll was mapped using satellite remote sensing techniques in conjunction with detailed in situ ground-referencing conducted over a 3.5 week period with the aim of creating large-scale, high resolution habitat and bathymetry maps. A series of closed loop levelling surveys were undertaken to establish the relative positioning of a network of five benchmarks around the Research Station, providing a common vertical datum against which the bathymetric map could be referenced. Eight habitat groupings were identified in the lagoon, with the two dominant classes mapped being "sparse macroalgae and seagrass assemblage on sand" and "dense macroalgal mat on sand", which covered 35% and 33% of the lagoon area respectively. Variations in lagoon floor elevation range from -0.2 to -30 m. Much of the lagoon is a flat, shallow (<3 >m) platform and the deepest areas are associated with the channels, particularly Grande Passe in the northwest. These maps represent a detailed record of the contemporary lagoon character against which future change of the lagoon environment can be monitored.