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Salt marshes are very valuable and threatened ecosystems, and are challenging to study due to their difficulty of access and the alterable nature of their soft soil. Remote sensing methods in unmanned aerial vehicles (UAVs) offer a great opportunity to improve our knowledge in this type of complex habitat. However, further analysis of UAV technology performance is still required to standardize the application of these methods in salt marshes. This work evaluates and tunes UAV-photogrammetry and UAV-LiDAR techniques for high-resolution applications in salt marsh habitats, and also analyzes the best sensor configuration to collect reliable data and generate the best results. The performance is evaluated through the accuracy assessment of the corresponding generated products. UAV-photogrammetry yields the highest spatial resolution (1.25 cm/pixel) orthomosaics and digital models, but at the cost of large files that require long processing times, making it applicable only for small areas. On the other hand, UAV-LiDAR has proven to be a promising tool for coastal research, providing high-resolution orthomosaics (2.7 cm/pixel) and high-accuracy digital elevation models from lighter datasets, with less time required to process them. One issue with UAV-LiDAR application in salt marshes is the limited effectiveness of the autoclassification of bare ground and vegetated surfaces, since the scattering of the LiDAR point clouds for both salt marsh surfaces is similar. Fortunately, when LiDAR and multispectral data are combined, the efficiency of this step improves significantly. The correlation between LiDAR measurements and field values improves from R² values of 0.79 to 0.94 when stable reference points (i.e., a few additional GCPs in rigid infrastructures) are also included as control points. According to our results, the most reliable LiDAR sensor configuration for salt marsh applications is the nadir non-repetitive combination. This configuration has the best balance between dataset size, spatial resolution, and processing time. Nevertheless, further research is still needed to develop accurate canopy height models. The present work demonstrates that UAV-LiDAR technology offers a suitable solution for coastal research applications where high spatial and temporal resolutions are required.