Abstract Burrow characteristics and bioturbation activities of benthic organisms play a key role in mangrove ecosystem biogeochemical and sedimentary functioning. In this study, we aimed to understand how small-scale topographic variations in a mud bank might influence burrow morphology and distribution in a French Guiana pioneer mangrove system (Sinnamary estuary), and to upscale spatial patterns using remote sensing. We used burrow resin casting and sediment conductivity measurements to depict subsurface 3D burrow structures. We found that the spatial heterogeneity of burrow sizes (small, medium, large) and morphologies (simple I- and J-shape, complex geometries) depended on the geomorphic units within mudflats (platform, channel, depression). The aperture areas of burrow casts were used to predict the volume and complexity of each burrow type, enabling us to use drone-derived burrow opening distribution maps to calculate burrow volumes and complexity at the mudflat scale. There are clear associations between tidal channels and depressions and voluminous, multi-aperture, complex and multi-species burrows. In contrast, simple I- and J-shaped burrows inhabited by single species were mainly found on platforms. These relationships lead to a comparatively large volume of tidal-irrigated and deeply aerated sediments connected to channels and depressions compared to platform areas. We suggest that, depending on their morphology and connectivity with the topography, burrows may exhibit differences in biogeochemical functioning depending on the geomorphic unit. We warn against generalizing the functioning of mangrove ecosystems across geomorphic units where impacts may differ. Further studies are needed to understand how different burrow morphologies and life cycles may alter hydrological, sedimentary and biogeochemical functioning.