This study comparatively assesses the Municipal Emission Reduction Plans (MERPs) of Spetses, Platanias, and Souli, emphasizing the role of water infrastructures in shaping municipal carbon footprints. Using secondary data extracted from the officially approved MERPs, a descriptive inter-municipal comparative analysis was conducted based on demographic variables and sectoral and total greenhouse gas emissions for the base year 2019 and the reference year 2023. Percentage changes in population and sector-specific emissions were calculated at the municipal level and subsequently compared across the three municipalities. The analysis covers municipal buildings and lighting, transport, waste and wastewater management, water and irrigation distribution systems, while also presenting the emission reduction actions and projected 2030 targets documented in the respective plans. The results reveal substantial inter-municipal variations, driven primarily by water supply models, geomorphology, altitude differences, network extent, and the distribution of service responsibilities. In Platanias and Souli, water supply and irrigation constitute among the most energy-intensive sectors, contributing significantly to total emissions, whereas in Spetses the externalized water supply model alters the emission structure. The findings indicate that water infrastructure can represent a significant emission source and that effective mitigation depends on spatially tailored strategies considering geomorphological, operational, and administrative characteristics.