Nanocomposite membranes (NCMs) provide inspiration to combine the superiorities of inorganic nanomaterials and polymeric matrices for outstanding nanofiltration performance. Herein, novel NCMs have been fabricated via co-deposition of polydopamine (PDA), polyetheylenimine (PEI) and electropositive gold nanoparticles (GNPs) followed by crosslinking. The GNPs distribute in the formed selective layer uniformly without obvious aggregation due to their good dispersion and compatibility with the positively charged PDA/PEI matrix. Thus the selective layer remains defect-free and the surface potential is enhanced by the positively charged GNPs. These endow the NCMs with high retention ratio (> 90%) for bivalent cations, such as Mg2+, Ca2+, and various heavy metal ions. Meanwhile, the permeate flux of the NCMs doubles compared with the PDA/PEI co-deposited nanofiltration membranes (NFMs) attributed to the hydrophilicity of the embedded GNPs and the loosened selective layer structures. The compact resistance and the structural stability of the NCMs are also improved effectively in contrast with the PDA/PEI ones, which are of significant importance for the practical use of NFMs. Moreover, the quaternary amine moieties on GNPs improve the antibacterial activity of NCMs against S. aureus and E. coli.