Characterisation of the ecosystem functioning of mudflats requires insight on the morphology and facies of these coastal features, but also on biological processes that influence mudflat geomorphology, such as crab bioturbation and the formation of benthic biofilms, as well as their heterogeneity at cm or less scales. Insight into this fine scale of ecosystem functioning is also important as far as minimizing errors in upscaling are concerned. The realisation of high-resolution ground surveys of these mudflats without perturbing their surface is a real challenge. Here, we address this challenge using UAV-supported photogrammetry based on the Structure-from-Motion (SfM) workflow. We produced a Digital Surface Model (DSM) and an orthophotograph at 1 cm and 0.5 cm pixel resolutions, respectively, of a mudflat in French Guiana, and mapped and classed into different size ranges intricate morphological features, including crab burrow apertures, tidal drainage creeks and depressions. We also determined subtle facies and elevation changes and slopes, and the footprint of different degrees of benthic biofilm development. The results generated at this scale of photogrammetric analysis also enabled us to relate macrofaunal crab burrowing activity to various parameters, including mudflat elevation, spatial distribution and sizes of creeks and depressions, benthic biofilm distribution, and flooding duration. SfM photogrammetry offers interesting new perspectives in fine-scale characterisation of the geomorphology, benthic activity and degree of biofilm development of dynamic muddy intertidal environments that are generally difficult of access. The main shortcomings highlighted in this study are a drift of accuracy of the DSM outside areas of ground control points and the deployment of which perturb the mudflat morphology and biology, the water-logged or very wet surfaces which generate reconstruction artefacts through the sun glint effect, and the time-consuming task of manual interpretation of extraction of features such as crab burrow apertures. On-going developments in UAV positioning integrating RTK/PPK GPS solutions for image-georeferencing and precise orientation with high-quality inertial measurement units will limit the difficulties inherent to ground control points, while conduction of surveys during homogeneous cloudy conditions could reduce the sun-glint effect. Manual extraction of image features could be automated in the future through the use of deep-learning algorithms.