Nanofiltration (NF) membrane can efficiently remove the ions from groundwater, especially for high valence ions. Results show that the removal rate of fluoride was approximately 67% by the NF system, while for arsenic the removal rate was more than 93%. NF presented the well selective removal for fluoride. The quality of product water meets the national drinking water standards. Therefore, the application of nanofiltration technology can significantly improve the drinking water environment of rural areas, avoiding the secondary pollution caused by other chemical treatment processes. The water product cost of NF technology is about RMB 0.026 yuan per liter, application of the process of 2:1 NF membranes arrangement for toxic or harmful ions removal from groundwater, including investment cost and operating cost. Therefore, NF technology for harmful ions removal is more economical than the price of the market bottled water and suitable for application in rural areas of China.