Coral reefs are particularly valuable marine ecosystems in terms of biodiversity and socio-economic factors. They are also some of the most vulnerable and threatened of global ecosystems, particularly in the view of unprecedented anthropogenic-driven disturbances. Understanding coral reef evolution is not straightforward, as these are complex systems where biological, physical and chemical processes continually interact over a range of spatial and temporal scales. Mapping the geomorphology of coral reefs has provided key information to scientists and managers about the distribution and extent of reef landforms giving insights into CaCO3 productivity and reef growth. Coral reef dynamics at geomorphological scales bridge the temporal and spatial gap between long-term geological and short-term ecological processes. The geomorphology of coral reef in Torres Strait remains uncharted at a detailed level despite being a northern extension of the GBR, the largest and most studied coral reef system in the world. A suite of geospatial techniques were used to investigate and extend existent morphological analysis and a carbonate budget for the emerged Sue reef, including the productive forereef. An approximated 19,432 t CaCO3 yr-1 were estimated for the whole platform, yielding an average gross productivity rate of 1.81 kg CaCO3 kg m2. A combination of data collection methods, including multibeam echosounding and optical remote-sensing derived bathymetry were used to analyse the complex terrain of the submerged Bet reef. A carbonate budget was estimated for the complete reef, amounting to an approximated 30,801 t CaCO3 yr-1, yielding an average gross productivity rate of 3.14 kg CaCO3 kg m2. Insights into carbonate and sediment dynamics between these different reef types were used to extrapolate CaCO3 productivity rates across Torres Strait. Innovative classification and spatial analysis techniques were used to accurately map the intrareef geomorphology of reefs, which was used as a basis to extrapolate CaCO3 production and derive a regional carbonate budget for Torres Strait. A maximum total vi of 9.6 million tonnes CaCO3 yr-1 were estimated for the region, averaging a value of 4.1 kg CaCO3 kg m2, almost twice the 2.4 CaCO3 kg m2 productivity rate estimated for the Great Barrier Reef Region.