Sufficient efforts have been carried out to fabricate highly efficient graphene oxide (GO) lamellar membranes for heavy metal ion separation and desalination of water. However, selectivity for small ions remains a major problem. Herein, GO was modified by using onion extractive (OE) and a bioactive phenolic compound, i.e., quercetin. The asprepared modified materials were fabricated into membranes and used for separation of heavy metal ions and water desalination. The GO/onion extract (GO/OE) composite membrane with a thickness of 350 nm shows an excellent rejection efficiency for several heavy metal ions such as Cr 6+ (∼87.5%), As 3+ (∼89.5%), Cd 2+ (∼93.0%), and Pb 2+ (∼99.5%) and a good water permeance of ∼460 ± 20 L m −2 h −1 bar −1 . In addition, a GO/quercetin (GO/Q) composite membrane is also fabricated from quercetin for comparative studies. Quercetin is an active ingredient of onion extractives (2.1% w/w). The GO/Q composite membranes show good rejection up to ∼78.0, ∼80.5, ∼88.0, and 95.2% for Cr 6+ , As 3+ , Cd 2+ , and Pb 2+ , respectively, with a DI water permeance of ∼150 ± 10 L m −2 h −1 bar −1 . Further, both membranes are used for water desalination by measuring rejection of small ions such as NaCl, Na 2 SO 4 , MgCl 2 , and MgSO 4 . The resulting membranes show >70% rejection for small ions. In addition, both membranes are used for filtration of Indus River water and the GO/Q membrane shows remarkably high separation efficiency and makes river water suitable for drinking purpose. Furthermore, the GO/QE composite membrane is highly stable up to ∼25 days under acidic, basic, and neutral environments as compared to GO/Q composite and pristine GO-based membranes.