Urban estuaries are an important interface between the land and sea where large amounts of terrestrial carbon and anthropogenic inputs are deposited from the catchment. Along the estuary, carbon is released as CO2 to the atmosphere and is buried or transformed before being discharged into the coastal ocean. Studies on carbon budgets are an important contribution to our understanding of how carbon is transformed within estuaries reflecting the human pressures on the ecosystem. Hence, such studies are fundamental to the sustainable management of urban estuary environments. The Sydney Harbour Estuary is a large complex drowned river valley system situated adjacent to the global city of Sydney that, by 2100, will have grown from 5 million to megacity status (10 million) with all the consequences of urbanisation having an impact on the harbour. There are no previous studies to provide an understanding of these impacts on the carbon cycle of the estuary, making this an important and challenging region to explore the carbon dynamics for the first time. In this study, the Sydney Harbour Estuary is investigated to determine if it is a net carbon sink (autotrophic) or source (heterotrophic) on an annual basis and to provide a measure to compare and contrast with global harbours/estuaries worldwide.