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Nanofiltration (NF) membrane configuration for fluoride and arsenic removal from groundwater has a key role in controlling operation performances and membrane fouling. Some bench-scale contrast experiments using commercial NF membranes were done to obtain the optimum arrangement performances. The NF membrane arrays included one-stage, two-stage, and three-stage systems. The NF membrane surface was negatively charged above its isoelectric point (approximately at pH 5.9–6.4). Accordingly, the raw groundwater was initially adjusted to a neutral or alkaline pH to enhance the effect of electrical charge repulsion and improve the ion removal efficiencies by NF. The encouraging results indicated that a membrane in a parallel-linear arrangement with staging 2:1 was the preferable arrangement to remove fluoride and arsenic from low-salinity groundwater in rural areas of China. With this optimal arrangement, the NF system obtained fluoride and arsenic removal efficiencies of 70˜73% and 92˜94% respectively, a preferable permeate flux of 73.37 L h−1m2and acceptable water flux recovery rate of 65% at 16°C. This optimal arrangement can further limit the potential membrane fouling by lowering the interstage Reynolds number. Moreover, the water product cost was lowest by the NF system with this optimal arrangement. [ABSTRACT FROM AUTHOR]