The Mediterranean marine communities are facing both anthropogenic pressures and biogeochemical disturbances. Internationalguidelines pursue the importance of preserving benthic environments, where a wide number of habitat-forming species is currentlythreatened. Monitoring provides essential information for mapping the ecological status of underwater environments and quantifyingthe impact of global changes on marine species. Detecting the health status of endangered marine species demands a high degreeof accuracy and fine-scale resolution. Large-scale and long-term monitoring activities require processing an increasing amount ofdata; analyzing such streams is hard to be sustained without automation.The main goal of the EUPHROSYNE research project lies in improving, testing and validating both in the laboratory and in the openwater a multi-sensor measuring system based on the integration of photogrammetry and fluorescence imagery. The project alsoincludes the development of AI (artificial intelligence), computer vision and geometry processing algorithms for automating dataanalysis. High-resolution surveys will enable the development of novel digital analysis, such as the assessment of species healthstatus at a fine scale using fluorescence, and the measurement (polyps, surface areas or volumes) of massive shaped coral digitaltwins using ad hoc geometry processing techniques. Moreover, AI processing techniques allow the fast non-destructive extraction ofrelevant biometric quantities from benthic communities from large datasets (such as the time series of orthoimages for long-termmonitoring or orthoimages coming from mapping large areas).EUPHROSYNE experiences the benefits of using SCUBA divers and underwater remotely operated vehicles (UROVs) for datacapturing, with the aim of fostering their adoption in ecology applications. Combining these emerging techniques (that can beapplied to a range of 3D morphometrics, different habitats, and species) paves the way to innovative opportunities in ecologicalresearch and more effective results than traditional in-situ measurements. The case studies will be Mediterranean habitat-forminganthozoans of international conservation interest sensitive to climate alterations and threatened by anthropogenic pressures actingat local scales (e.g.pollution, recreational SCUBA diving, fishing gears, and boating). EUPHROSYNE will contribute to the developmentand empowering of innovative procedures, algorithms and methods to improve underwater survey techniques and detect changes in biological systems, fostering the targets of the European Green Deal and EU Biodiversity strategy.