Limited water resources and greenhouse gas emissions from fossil fuels used in electricity production are problems experienced in Chile. To address water shortages, many copper mining companies have started to use seawater or desalinated water in their operations. However, seawater exerts a negative impact on the mineral processing operation. It reduces the recovery of copper and molybdenum minerals in the flotation of copper molybdenum sulfide ores due to the presence of calcium and magnesium ions. This study aims to propose a partial desalination treatment for calcium and magnesium species removal to improve the recovery of valuable minerals in the flotation of copper molybdenum sulfide ores. The proposed method uses carbon dioxide gas and sodium greenhouse gas emissions. hydroxide to promote the removal of calcium and magnesium ions from seawater. As a result, the partial desalination treatment can remove 60.5% of calcium and 98.3% of magnesium species. In addition, it helped in reaching a high recovery of molybdenum (81.1%) and copper (93.4%) as well as depressed pyrite (0.95% of iron) in the flotation of copper-molybdenum sulfide ores. Therefore, partial desalination treatment could provide the appropriate water quality required in the froth flotation process and it could reduce carbon dioxide from greenhouse gas emissions.