Lagoons and coral reefs are of great biological, ecological, and economic value, while suffering from anthropogenic and environmental pressures. Until a few years ago, monitoring methods for shallow water ecosystems were limited to in situ surveys and/or analysis of satellite remote sensing data. However, in situ methods are time consuming and expensive while they are liable to space limitations. Moreover, high-resolution satellite imagery is equally costly in terms of data acquisition and strongly dependent on meteorological conditions (rain, clouds, tides etc.). The advent of Unmanned Aerial Vehicles (UAVs) provides new opportunities to monitor large-scale coastal ecosystems through the ability to capture centimeter-resolution 3D data, which is impossible with conventional approaches. At the same time, UAVs have the advantage of performing low-cost repeated campaigns during the lowest tides. In this framework, the current study compares UAV imagery to very high-resolution satellite data covering lagoon reefs and investigates the role of UAV-derived products such as Digital Surface Models (DSMs) and orthophotos in the evolution of such environments over time. Prokopos Lagoon located in Western Greece was selected as a study area. In recent decades, it has been observed that the POLYCHAETE Ficopomatus enigmaticus has formed large reefs, covering a significant part of the lagoon extent. In light of this, images collected with a vertical takeoff and landing UAV were compared to Pleiades multispectral data. Both data sets were evaluated in terms of accuracy and long-term monitoring capability. As expected UAV data proved to be more effective than the Pleiades data for the precise monitoring of polychaete expansion. Within a year, the polychaete formations extent was doubled in the north part of the lagoon.
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