Coastal marine ecosystems of the Mediterranean Sea, such as coralligenous habitats, play a crucial role in biodiversity and ecosystem services. However, they are increasingly threatened by anthropogenic pressures and climate change, highlighting the urgent need for innovative strategies to ensure their protection. This study supports the development of a Digital Twin of the Ocean (DTO), aimed at creating a digital representation of the marine ecosystem. Continuously updated with experimental data, the DTO serves as a tool to support conservation and management activities (e.g., identifying the most suitable areas for restoration). A key component of the DTO is the availability of water column data and benthic observations, which allow for the ongoing validation of the digital model, enabling the creation of realistic “what if scenarios.” This activity stems from two complementary projects: EFFECTIVE, which aims to develop scientific knowledge and integrated guidelines for applying Ecosystem-Based Management to the protection of the Mediterranean’s Blue Natural Capital; and RENOVATE, which focuses on restoring ecosystem services compromised by the development of the Port of Civitavecchia through active and passive compensation measures. This study presents the measurement activities supporting the development of the DTO in two restoration areas of the coralligenous biocenosis (Habitat 1170). Using scuba divers, CTD stations, and autonomous mobile platforms, key data were collected for the study of the habitat and validation of the DTO. These data include continuous seabed temperature measurements to identify the duration, frequency, and intensity of potential marine heat wave events; CTD profiles to monitor water column stratification; and total suspended solids (TSS)/turbidity, a parameter that significantly affects the life of benthic organisms. This information supports the ecological assessment of the sites and the validation of digital models useful for planning restoration interventions.