Habitat structural complexity plays a key role in the dynamics and resilience of coral reef communities. The critical situation of coral reef ecosystems beseeches a rapid improvement of monitoring tools to assist in the implementation of efficient conservation measures. Today, new reef assessment technologies support researchers and managers to collect information safer, faster, and with greater accuracy. Among them, photogrammetry by Structure-from-Motion (SfM) creates three-dimensional models and reef zone maps from overlapping images to conduct quantitative surveys of benthic communities. This thesis addressed four objectives: 1) define underwater photogrammetry protocols to create 3D models of coral colonies and reefscapes, in order to conduct physical and ecological assessments, 2) develop new quantitative reef habitat descriptors, 3) determine the links between these descriptors and the key functional processes ensured by associated fish assemblages, 4) compare photogrammetric methods with a traditional monitoring method, the Line Intercept Transect (LIT). Overall, 120 coral colonies, 24 reefscapes, and two artificial structures (breakwaters) were 3D modeled in two biogeographic provinces: New Caledonia (Pacific Ocean), Europa Island, and Reunion Island (Indian Ocean). Two photogrammetric protocols were defined corresponding to the study scales: the coral colony (≤ 2 m3) and the reefscapes and breakwaters (> 100 m2). Analyzing the 3D models of coral colonies provided 2D and 3D metrics to estimate their shelter volume. Predictive models were then built and fitted to estimate shelter capacity at the reefscape scale. Mapped reefscapes provided the necessary information to calculate 22 new quantitative descriptors. Among them, seven were the most complementary: surface complexity, shelter capacity, diversity of shelter - Shannon Shelter Index, the abundance of branching, massive and tabular, and total coral cover. They explained 63% and 70% of the distribution of reef fish biomass and abundance, respectively. Multifactorial analyses demonstrated the importance of these habitat descriptors in supporting five key functions of reef ecosystems that are ensured by groups of fishes (herbivory-bioerosion, secondary production, plankton assimilation, predation, and coral feeding). Comparisons between photogrammetric methods and the LIT method showed that the surface analysis on the orthomosaics is the most efficient method considering the quantity and quality of data that can be gathered and the time expenditure. The LIT method is less time-consuming and more efficient for specific taxonomic identifications, though it is the most limited method in terms of descriptors and the representativeness of the ecosystem. In addition to the four principle objectives, the 3D models and other photogrammetric outputs served as communication tools in different awareness actions.To sum up, this thesis demonstrated the relevance of underwater SfM photogrammetry applications for coral reef studies, management, and awareness actions. The collected data and their analyses also contribute to establishing a baseline for monitoring the state of reef ecosystems and their functions. In doing so, it provides new scientific information to enhance future management measures and confront the ambitious twenty-first-century conservation targets.