This document compose the Project Management Guide (PMG) of the eDNAqua-Plan, which is implemented under the framework of the European Commission (EC) Horizon Europe funding programme dedicated to research and innovation. The eDNAqua-Plan PMG serves as a reference document for all project members, notably outlining: i) the summary of the goals and objectives of the project; ii) the details of the project management and governance (organizational structure), roles and responsibilities of the participants; iii) the definition of the main communication channels; iv) the procedures and management tools implemented to ensure the successful completion of the project (i.e., schedule, reporting, financial guide, etc.). The guide is based on the terms and conditions agreed under the Grant Agreement and the Consortium Agreement to help all partners comply with the agreements.