The Great Barrier Reef is the largest complex of coral reefs and associated habitats on Earth (Figure 1.1). The ecosystem extends for over 2,200 kilometres along the north-eastern coast of Australia, containing around 2,900 coral reefs and representing one of the most biologically diverse ecosystems known to exist (Hutchings et al., 2009; GBRMPA, 2013). Although there has been some debate about the age of the ecosystem and of its more ancient foundations, the modern Great Barrier Reef is a young structure in geological terms, having formed during the last 10,000 years of the Holocene epoch (Hopley, 2009; Hopley et al., 2007). Consequently, its modern reefs have always existed in relation to humans, supporting the subsistence economies of coastal Indigenous Australians and containing many places of cultural and spiritual significance. After European settlement commenced in Australia, the ecosystem played an important role in the colonial development of Queensland and its resources were subjected to more intensive exploitation (Bowen, 1994; Bowen and Bowen, 2002).