The Life Cycle Assessment (LCA) system, which can be used as a decision support tool for managing environmental sustainability, includes carbon footprint assessment as one of the available methodologies. In this study, a carbon footprint assessment was used to investigate seawater production systems of a desalination plant in Senok, Kelantan, Malaysia. Three stages of the desalination plant processing system were investigated and the inventory database was developed using the relevant model framework. Subsequently, measurements and interpretations were performed on several key indicators such as greenhouse gases, energy efficiency, acidic gases, smog, and toxic gases. Overall, the results of the study indicate that the Reverse Osmosis (RO) technology that is used in the desalination plant in the study area is one of the best options to meet the demands of the environmental sustainability agenda (SDGs). This is due to the lower carbon dioxide (CO2) emission, of about 3.5 × 10−2 kg of CO2 eq per m3/year, that was recorded for the entire operation of the system. However, several factors that influence important errors in carbon footprint decisions, such as the lack of EIA reporting data and the literature on carbon footprint in the Malaysian scenario, in addition to direct and indirect carbon input calculations, need to be identified in more detail in future research.