Micropollutants in freshwater, e.g., pharmaceuticals such as contraceptives, are a source of increased concern for human health and wildlife. Even after excretion, some of these compounds are pharmaceutically active in aquatic environment and they are found to cause endocrine disruption in both human and wildlife populations. In this study we analyzed a membrane system, coated with enzymes, which removes endocrine disrupting chemicals or micropollutants from surface water used for drinking. In order to help a membrane manufacturer in product development, we conducted a cradle-to-grave life cycle assessment. Water purification with two membrane systems, based on membrane coating covalent binding versus adsorption, were analyzed and compared with granulated activated carbon made from coal and wood. It was found that the membrane with covalent binding can have much lower environmental impacts than activated carbon made from coal. A sensitivity analysis showed that operational electricity use, the source of electricity and membrane coating frequency influence the results significantly. Scenario analysis indicates that a membrane system with covalent binding which uses operational electricity lower than 0.2 kWh per m3 of filtered water and with monthly enzyme coating frequency can perform better than conventional activated carbon systems irrespective of the electricity source. These findings can be used to guide the optimization of the membrane parameters. This study provided an understanding of the membrane modification for micropollutant removal and its impacts on environment. Finally, we describe how environmental sustainability can be integrated into business decisions, such as process and material selection and design optimization, with the help of life cycle assessment.