Technology plays a key role in advancing global research. Since the 1960s, environmental scientists have progressed from human observations and paper-based calculations to remote sensing and high-performance computing data analyses. Despite the monumental advances in statistical and computational approaches, the generation of raw field data quantifying baseline ecological states of benthic communities still relies on in situ visual surveys using transect- or plot-based approaches. Limitations of these approaches are clear for marine applications. Underwater survey efforts are innately more restricted than terrestrial counterparts because of human physiological capacities. To maximise the efficiency of underwater surveys, structure from motion (SfM) three-dimensional (3D) model reconstructions and two-dimensional (2D) orthomosaics have been developed recently. These approaches are repeatable and substantially increase survey area and data volume per unit time and effort invested. By conducting SfM surveys at multiple sites, we can uncover microhabitats and quantify spatial patterns of structural complexity and community structure of coral reef benthic organisms. Repeated SfM surveys allow for detailed assessments of community dynamics, including demography, growth rates and survival/mortality, and the correlation of these observations with environmental and ecological parameters. Here, we evaluate the capacity of SfM approaches through a case study from Moreton Bay, Queensland, Australia, where urbanisation, climate change and flooding have substantially altered ecosystem dynamics.