In addition to the potential global impact of climate change on marine ecosystems, the extensive use of high-impact fishing methods is a primary catalyst for benthic biodiversity degradation in the Mediterranean Sea. Implementing fishery no-take zones (FNTZs) emerges as a key measure for the sustainable recovery and management of overexploited stocks and habitats. To identify appropriate geographical scales for their implementation, it is crucial to understand the spatial connectivity of species and ecosystem functioning during long periods. Therefore, it is necessary to implement robust spatio-temporal multiparametric monitoring procedures, allowing the synchronous collection of biological (i.e., image-based), oceanographic and geochemical data. For this, we developed a spatial cooperative network of fixed (i.e., landers) and docked mobile (i.e., AUVs) platforms with wireless intercommunication capability (i.e., by acoustic modems). This system is designed for intelligent observation monitoring and mapping (i.e., AI-based recognition of species and bioturbation features) over extended periods with real-time, remote supervision and data transmission through the water column to an ASV.