Substrate complexity is strongly related to biodiversity in aquatic habitats. We illustrate a novel framework, based on Structure-from-Motion photogrammetry (SfM) and Multi-View Stereo (MVS) photogrammetry, to quantify habitat complexity in freshwater ecosystems from Unmanned Aerial Vehicle (UAV) and underwater photography. We analysed sites in the Xingu river basin, Brazil, to reconstruct the 3D structure of the substrate and identify and map habitat classes important for maintaining fish assemblage biodiversity. From the digital models we calculated habitat complexity metrics including rugosity, slope and 3D fractal dimension. The UAV based SfM-MVS products were generated at a ground sampling distance (GSD) of 1.20–2.38 cm while the underwater photography produced a GSD of 1 mm. Our results show how these products provide spatially explicit complexity metrics, which are more comprehensive than conventional arbitrary cross sections. Shallow neural network classification of SfM-MVS products of substrate exposed in the dry season resulted in high accuracies across classes. UAV and underwater SfM-MVS is robust for quantifying freshwater habitat classes and complexity and should be chosen whenever possible over conventional methods (e.g., chain-and-tape) because of the repeatability, scalability and multi-dimensional nature of the products. The SfM-MVS products can be used to identify high priority freshwater sectors for conservation, species occurrences and diversity studies to provide a broader indication for overall fish species diversity and provide repeatability for monitoring change over time.
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