A Gravity-driven membrane (GDM) system is one of the promising solutions for household drinking water treatment in the developing countries. In this study, the GDM system was tested for optimizing manual cleaning protocols using three different feed water solutions. Two types of manual cleaning were performed to delay the permeability decrease, cleaning between batches and long-term cleaning. The optimized cleaning between batches protocol was 3 twisting and 10 vertical shaking. And the optimized long-term cleaning protocol was 70 vertical shaking for both the middle region of the module and near the header part. These cleaning protocols allowed the system to produce sufficient water to meet the daily minimum water requirements for a 5-person family, even for using the wastewater influent. The system produced Escherichia coli free water.