This specification describes a method for lowering the content of monovalent ions in a final concentrate of a nanofiltration system relative to a brine and a corresponding nanofiltration system. The nanofiltration system comprises at least three stages of nanofiltration, wherein the concentrate from each segment flows into the next segment. A feed stream is sent into one stage to generate a concentrate stream, and a first portion of the concentrate stream is recirculated to the one stage. The pH of the feed stream is controlled in a range of 2-7. The temperature of the feed stream is in a range of 20-60° C. The feed stream includes the recirculated concentrate stream and at least part of a concentrate generated from an upstream stage. The method and the system described herein can reduce the concentration of monovalent ions in the final concentrate during a nanofiltration separation process.