Our understanding of Earth surface processes is rapidly advancing as new remote sensing technologies such as LiDAR and close-range digital photogrammetry become more accessible and affordable. A very-high spatial resolution digital terrain model (DTM) and orthophoto mosaic (mm scale) were produced using close-range digital photogrammetry based on ‘Structure-from-Motion’ (SfM) algorithms for a 250 m transect along a shallow coral reef flat on Heron Reef, Great Barrier Reef. The precise terrain data were used to characterise surface roughness, a critical factor affecting ecological and physical processes on the reef. Three roughness parameters, namely the root mean square height, tortuosity (or rugosity) and fractal dimension, were derived and compared in order to asses which one better characterises reef flat roughness. The typical relief across the shallow reef flat was 0.1 m with a maximum value of 0.42 m. Coral reef terrain roughness, as characterised by the three chosen parameters, generally increased towards the middle of the transect where live coral covers most of the reef flat and decreases towards the edges of the transect. The fractal dimension (values ranging from 2.2 to 2.59) best characterised reef roughness, as evidenced by a closer agreement with the distribution of known coral benthic substrates. This is the first study quantifying scale-independent roughness of a coral reef at benthic and biotope/patch levels (cm-m). The readily available and cost-effective methods presented are highly appropriate for data collection, processing and analysis to generate very-high spatial resolution DTMs and orthophoto mosaics of shallow and energetic coral reefs.