Lord Howe Island and Balls Pyramid are located approximately 600 km offshore of the southeastern Australian mainland, in the subtropical waters of the northern Tasman Sea. Lord Howe Island hosts the most southern coral reef in the Pacific Ocean, and the shelves surrounding both islands feature fossil coral reefs. This study creates a seamless, high-resolution (5 m cell size) bathymetry model of the two shelves to compare and contrast the extent of reef development and shelf morphology. This was produced by integrating satellite-derived depth data (derived to 35 m depth) and multibeam echosounder (MBES) data. Image partitioning and filtering improved the accuracy of the bathymetry estimates and the suitability for integration with MBES data. Diverse accretionary and erosional geomorphic features were mapped on both shelves, with fossil reefs dominating the shelves in 25–50 m depth. Similar patterns of shelf morphology were observed for the middle and outer shelves, while the inner shelf regions were most dissimilar, with reef development greater around Lord Howe Island compared to the more restricted inner shelf reefs around Balls Pyramid. Understanding the relative extent and morphology of shelf features provides insights into the geological and ecological processes that have influenced the formation of the shelves.