A nanomembrane-based hybrid treatment system for separation of fluoride from contaminated groundwater and its subsequent stabilization in a solid matrix through chemical coagulation–precipitation process using response surface optimization for safe disposal were designed and investigated. The continuous flat-sheet cross-flow nanofiltration membrane module with well-screened commercial polyamide composite membrane succeeded in removing 99 % fluoride from water while yielding a pure water flux as high as 158–160 L/m2h of a transmembrane hydraulic pressure of only 14 bars. Such an operating pressure is much lower than that required in reverse osmosis for the same separation. The designed system for the first time provides a total solution to a complex problem in a very simple, compact, flexible, and novel design that ensures continuous, steady, and hassle-free long-term operation without the necessity for frequent replacement of membranes. The approximate cost for production of 1000 L of safe drinking water from fluoride-contaminated groundwater computes to only $ 1.4, indicating affordability in adopting the low-cost, high-flux water purification system by the affected people in many parts of the world.