Implementing effective marine monitoring to detect and track ecosystem shifts, biodiversity alteration, and habitat loss is one of the most crucial challenges to meet the objectives set out by the Post-2020 Biodiversity Framework and by the United Nations Sustainable Development Goals. The lack of coordinated and harmonized monitoring frameworks at different spatial scales and their weakness in accounting for ecological processes, due to incomplete sets of monitoring variables, strongly hinder the achievement of conservation objectives. Here, we propose an approach to build a coherent ecosystem-based system of monitoring variables for target marine species and habitats. The approach is designed to integrate the existing monitoring frameworks set up by the Water and the Marine Strategy Framework directives, and the Essential Ocean and Biodiversity Variables, with the aim to contribute to their harmonization and implementation. Furthermore, by embracing a holistic vision, it aims to incorporate ecological processes and socio-ecological aspects, considering the benefits of public engagement through citizen science, and of the ecosystem services approach for policies’ implementation. The study stems from the Ecological Observing System of the Adriatic Sea (ECOAdS), which was developed in the framework of the Interreg Italy-Croatia project ECOSS, using as exemplary monitoring test cases two relevant conservation targets for Natura 2000 sites of the Adriatic Sea, the common bottlenose dolphin and seagrass meadows. We test the potential of this approach in guiding the prioritization of monitoring variables under ecosystem-based criteria, and provide insights into the benefits delivered by an integrated system of observatories’ networks and monitoring frameworks to support marine conservation at both local and regional scales. The proposed approach can be transferred to other contexts and scales to help build a common knowledge and monitoring framework for conservation and management strategies, saving costs by relying on available resources and on consolidated and long-lasting approaches that might converge towards global initiatives.