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The aim of the present paper is to propose a new methodology for the production and installation of green artificial reefs (GARs) in shallow waters, with special attention to the transport stages. The process includes both onshore (manufacturing, road transport and unload at port) and offshore (load at port, sea transport, positioning, and deployment tasks) stages. Two different types of truck were analysed for the road transport. Furthermore, three different options were considered for sea transport: a workboat powered by liquefied natural gas, a barge using diesel (0.1% sulphur) as fuel, and an electric specific design barge. A simulation tool called AGARDO (Automatic Green Artificial Reef Deploy Optimisation) was developed for such a purpose. An estuary located in Galicia (North-West of Spain), where 180 GAR units must be installed, has been considered as case study. AGARDO was used to obtain results concerning process total time, equivalent CO2 emissions and costs for different scenarios. Consequently, the use of the proposed methodology allows the decision-maker to select the best option in terms of costs, emissions and time. AGARDO can be easily adapted to other case studies, with different onshore and offshore options. [ABSTRACT FROM AUTHOR]