Changes to coral reef landscapes are driven by regional processes that are unique to particular localities, yet much of our knowledge about how landscape changes manifest in coral reef environments comes from specific locations. We compare observations of 45 years of change on reef-flat landforms, including sand cays and mangroves, associated with low wooded islands in Australia and Indonesia. We draw on remote sensing technology, including satellite images and unmanned aerial vehicle (UAV) surveys to provide high resolution aerial photomosaics and digital elevation models (DEMs) and field observations from ground referencing campaigns. Four low wooded island sites are compared; two in the Great Barrier Reef (GBR), Australia (Nymph Island and Two Isles) and two in the Spermonde Archipelago, Indonesia (Sabangko and Tanakeke Island). In particular, the Spermonde and GBR sites can be distinguished in relation to the process regime that entrains, distributes and deposits sediments on the reef surface thereby providing a substrate for further mangrove colonisation, particularly the presence or absence of cyclones as a key determinant of sediment transport. The influence of human populations inhabiting these sites is also an important control on their geomorphology. In the Spermonde Archipelago, local communities have altered sand cays through the development of infrastructure and converted mangroves to shrimp farms, while sand cays and mangroves have remained largely unaltered by humans on the GBR. This comparative evaluation of changes to sand cays and mangrove forest across low wooded islands emphasises the importance of considering changes within the context of their local geographic setting, inclusive of natural environmental and anthropogenic drivers of change.