AbstractThe calcareous Halimeda bioherms of the northern Great Barrier Reef, Australia are the largest actively accumulating Halimeda deposits worldwide. They contribute a substantial component of the Great Barrier Reef neritic carbonate factory, as well as the geomorphological development of Australia's northeast continental shelf. Halimeda bioherm geomorphology is complex, expressing three distinct variations in morphotype patterns: annulate, reticulate and undulate. Similar regular and irregular geomorphological patterning often results from scale‐dependent biophysical feedback mechanisms. Therefore, a better understanding of morphotype differentiation can inform the biotic and abiotic drivers of spatial heterogeneity in the bioherm ecosystem. Here, 3D LiDAR bathymetry is integrated with 2D sub‐bottom profile datasets to investigate surface topography and internal sedimentary architecture of Halimeda bioherms through space and time. Using the ESRI ArcGIS 3D Analyst and Benthic Terrain Modeller extensions, the bioherm surface and subsurface geomorphometric characteristics were quantified for the annulate, reticulate and undulate morphotypes. Significant variation was found between the three bioherm morphotypes in their surface topography, internal structure, volume, slope gradients and terrain complexity. Therefore, their geomorphology is probably influenced by differing processes and biophysical feedback mechanisms. The complex surface topography does not appear to be inherited from the antecedent substrate, and preferred aspect orientations resulting from hydrodynamic forcing appear to be limited. It is suggested here that autogenic dynamics or biotic self‐organization similar to patterns and processes in other marine organo‐sedimentary systems modulates Halimeda bioherm geomorphology, and some hypotheses are offered towards future studies. Morphotype differentiation has implications for the development of the Halimeda bioherm carbonate factory, rates of sediment aggradation and progradation, and variable capacity to fill accommodation space. Self‐organization dynamics and morphology differentiation in Modern bioherm systems could potentially inform palaeo‐environmental interpretations of fossil bioherms and phylloid algal mounds on geological timescales.