Loose nanofiltration membranes, which have a loose selective layer and desired surface charge, provide high water flux and significant retention of low molecular weight molecules. In this study, a thin film of copper (II)-benzene-1,3,5-tricarboxylate (Cu-BTC) clusters was anchored on the surface of a chitosan (CS)-coated polyethersulfone (PES) membrane to improve the surface properties as well as performance (permeability, heavy metal removal efficiency, and antifouling activity) of the membrane. Characterization techniques, such as FE-SEM, EDX, XPS and AFM, zeta potential and water contact-angle measurements, verified that Cu-BTC was successfully anchored on the CS layer. The Cu-BTC/CS membrane exhibited higher surface hydrophilicity and roughness compared to the pristine one. It also demonstrated a water flux of 44 L m−2h−1 and a manganese removal efficiency of 86%, while the membrane coated only with CS had an average water flux of 39 L m−2h−1 and a manganese removal efficiency of 78%. Compatibility and interfacial interactions between the Cu-BTC clusters and the CS layer were investigated using molecular dynamics (MD). MD simulations indicated that the Cu-BTC clusters increased the affinity of the membrane for water molecules. The anchored Cu-BTC clusters also improved the antibacterial activity of the membrane; the Cu-BTC/CS membrane inactivated 83% of Escherichia coli bacteria, while the pristine CS membrane 47% of the bacteria. The Cu-BTC/CS membrane also demonstrated interesting anti-fouling properties against both organic and biological foulants.