The World Heritage microbialites, coquinas, and microbialitic-sediments of Hamelin Pool, Shark Bay, Western Australia, form through complex community and environmental interactions resulting in surficial CO2 sequestration. Predicted climate-change impacts threaten the stability of this setting and the balance of biogeomorphological processes that generate them. In this setting, long-term surficial CO2 sequestration occurs through the combination of biomineralisation, organomineralisation and lithification, which locks atmospheric CO2 into CaCO3 rocks and sediments. Biogeomorphological processes that control the distribution and effectiveness of these mechanisms including biostabilisation, bioconstruction, bioerosion and bioturbation have not been addressed in this setting to date. A three-dimensional biogemorphological mapping unit framework is defined at three locations in Hamelin Pool within the shallow-subtidal to supratidal zones based on historical and recent multiscale datasets. This framework is used to review the complex distribution of geomorphological and biogeomorphological processes. The distribution of lithification within a biogeomorphological process context is examined, and current geological analogue models of microbialite and coquina development are expanded to include biogeomorphological processes. The framework is used to understand the impacts of increased water elevation in response to intensification of the Leeuwin Current during the 2010–2012 Ningaloo Niño event. Potential climate change impacts are identified including reduced intertidal bioconstruction, and a shift from microbialitic structure generation to increased grain generation reducing stromatolite development. Review of the uncertainty of impacts of ocean acidification and temperature shifts on biomineralisation, organomineralisation and lithification processes, crucial to the maintenance of the outstanding universal values in this World Heritage location, suggests urgent research is required.