Graphene oxide (GO) membranes have demonstrated significant potential in water desalination owing to their well-defined molecular sieving characteristics and ultrafast water transport pathways. However, their practical applicability under high-salinity conditions remains constrained by inherent challenges, including excessive membrane swelling, structural instability, and the trade-off between ion selectivity and water permeability. We demonstrate the intercalation of reduced graphene oxide (rGO) membranes with polyconjugated organic molecules as a systematic tailored approach to mitigate these limitations and enhance desalination performance. The incorporation of these molecular intercalants not only modulates the interlayer characteristics of rGO nanosheets but also improves structural integrity, thereby optimizing ion exclusion mechanisms. Detailed structural characterization and realistic permeation measurements on these intercalated rGO membranes under high-salinity conditions (such as 0.5 M NaCl and Na2SO4) reveal remarkable enhancements in inorganic salt rejection while maintaining water permeability. These findings underscore the potential of intercalation engineering as a robust strategy for developing next-generation graphene-based membranes for water processing under realistic operating conditions. Notably, the selected polyconjugated organic molecules also offer key advantages such as commercial availability and facile integration without the need for complex organic synthesis, rendering them viable for scalable membrane fabrication.