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Aquatic ecosystems are crucial in preserving biodiversity, regulating biogeochemical cycles, and sustaining human life; however, their resilience against climate change and anthropogenic stressors remains poorly understood. Recently, unmanned aerial vehicles (UAVs) have become a vital monitoring tool, bridging the gap between satellite imagery and ground-based observations in coastal and marine environments with high spatial resolution. The dynamic nature of water surfaces poses a challenge for photogrammetric techniques due to the absence of fixed reference points. Addressing these issues, this study introduces an innovative, efficient, and accurate workflow for georeferencing and mosaicking that overcomes previous limitations. Using open-source Python libraries, this workflow employs direct georeferencing to produce a georeferenced orthomosaic that integrates multiple UAV captures, and this has been tested in multiple locations worldwide with optical RGB, thermal, and multispectral imagery. The best case achieved a Root Mean Square Error of 4.52 m and a standard deviation of 2.51 m for georeferencing accuracy, thus preserving the UAV's centimeter-scale spatial resolution. This open-source workflow represents a significant advancement in the monitoring of marine and coastal processes, resolving a major limitation facing UAV technology in the remote observation of local-scale phenomena over water surfaces. [ABSTRACT FROM AUTHOR]

Oysters support an economically important fishery in many locations in the United States and provide benefits to the surrounding environment by filtering water, providing habitat for fish, and stabilizing shorelines. Changes in oyster reef health reflect variations in factors such as recreational and commercial harvests, predation, disease, storms, and broader anthropogenic influences, such as climate change. Consistent measurements of reef area and morphology can help effectively monitor oyster habitat across locations. However, traditional approaches to acquiring these data are time-consuming and can be costly. Unoccupied aircraft systems (UAS) present a rapid and reliable method for assessing oyster habitat that may overcome these limitations, although little information on the accuracy of platforms and processing techniques is available. In the present study, oyster reefs ranging in size from 30 m2 to 300 m2 were surveyed using both fixed-wing and multirotor UAS and compared with ground-based surveys of each reef conducted with a real-time kinematic global positioning system (RTK-GPS). Survey images from UAS were processed using structure from motion (SfM) stereo photogrammetry techniques, with and without the use of ground control point (GCP) correction, to create reef-scale measures of area and morphology for comparison to ground-based measures. UAS-based estimates of both reef area and morphology were consistently lower than ground-based estimates, and the results of matched pairs analyses revealed that differences in reef area did not vary significantly by aircraft or the use of GCPs. However, the use of GCPs increased the accuracy of UAS-based reef morphology measurements, particularly in areas with the presence of water and/or homogeneous spectral characteristics. Our results indicate that both fixed-wing and multirotor UAS can be used to accurately monitor intertidal oyster reefs over time and that proper ground control techniques will improve measurements of reef morphology. These non-destructive methods help modernize oyster habitat monitoring by providing useful and accurate knowledge about the structure and health of oyster reefs ecosystems. [ABSTRACT FROM AUTHOR]