Chitosan functionalized (CoFe2O4−CuO) composite nanoparticles were synthesized and then used in fabrication of PES-based nanofiltration membranes. X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscopy were used for the characterization of synthesized nanoparticles. The fabricated membranes were also characterized by scanning electron microscopy, 3D surface images, water contact angle, membrane porosity, pure water flux, salt rejection and fouling resistance consideration. Obtained results revealed that water contact angle was reduced significantly from 65° for the neat membrane to 36° for M5 with 1.0 wt% composite nanoparticles. All modified membranes also showed higher water flux and salt rejection than virgin PES membrane. The highest pure water flux measured 45.2 L/m2h and the highest salt rejection measured 88% for the modified membranes containing of composite nanoparticles. The modified membranes showed outstanding antifouling ability. The flux recovery ratio enhanced from 40% for pristine membrane to 93% for the modified ones with 0.5 wt% of Cs-functionalized (CoFe2O4/CuO) composite nanoparticles.