The coexistence and interaction of monovalent selective electrodialysis membranes with real brines prompt us to investigate the mechanistic insights into the deterioration in separation efficiency of membranes for their practically long-term applications. In this work, the polyethyleneimine (PEI)/poly(styrene-divinylbenzene) (PS-DVB) monovalent selective ion exchange membrane (IEM) was exposed to the brines from Llullaillaco Salt Lake (Argentina) with highly concentrated total dissolved solids (TDS) for the practically long-term operation for up to 30 days. A concurrent degradation of surface nanostructure and charge functionalization of the IEM membrane occurred, leading to a decreased mono-/divalent permselectivity from 16.60 to 5.67 (i.e., K + /Mg 2+ ), before/after being treated by real brines (409 g/L TDS concentration). The declined separation property is believed to be attributable to the surface degeneration, because of the reduction in electrostatic interactions between the PEI active layer and the PS-DVB support. This is caused by the amassed ions that disturb and/or even destroy the ionic crosslinking interactions between oppositely charged ammonium- (PEI) and sulfonate-based (PS-DVB) polyelectrolytes. From these findings in this study, we develop a fundamental understanding to unveil the decomposition of the ionic crosslinking network of monovalent selective IEMs, within highly salinity solutions, offering guidance for the electrodialysis practical applications, but beyond the salt lake brines. • The separation efficiency declines over long-term operations by real brines. •Treatment by higher salinity brines causes more serious degeneration. •The K + /Mg 2+ permselectivity decreased from 16.60 to 5.67. •Amassed ions disturb ionic crosslinking interactions between layer and substrate.