The multilateral failure to apply the Convention on Biological Diversity (CBD) by the target year 2010 was headline news as are the accelerating climatic changes which dictate its urgency. Some ecosystems that are vulnerable to anthropogenic change have few species listed as endangered because too little is known about their biota. The highest vulnerability may correspond to where hotspots of species endemism, range limits and physiological sensitivity overlap with areas of most rapid physical change. The old, large and remote archipelago of South Georgia is one such location. Sea-surface temperatures around South Georgia are amongst the most rapidly warming reported. Furthermore oceanographic projections are highlighting the region as extremely vulnerable to ocean acidification. We outline the first polar Darwin Initiative project and the technical advances in generating an interactive and fully integrated georeferenced map of marine biodiversity, seabed topography and physical oceanography at South Georgia. Mapping marine mega and macro-faunal biodiversity onto multiple physical variables has rarely been attempted. This should provide a new tool in assessing the processes driving biological variability, the importance of marine areas in terms of ecosystem services, the threats and vulnerabilities of Polar Regions and should greatly aid implementation of the CBD.