In the present work, chemically modified graphene oxide (GO) was incorporated as a crosslinking agent into thin-film composite (TFC) nanofiltration (NF) membranes for water desalination applications, which were prepared by the interfacial polymerization (IP) method, where the monomers were piperazine (PIP) and trimesoyl chloride (TMC). GO was functionalized with monomer-containing groups to promote covalent interactions with the polymeric film. The composite GO/polyamide (PA) was prepared by incorporating amine and acyl chloride groups into the structure of GO and then adding these chemical modified nanomaterial during IP. The effect of functionalized GO on membrane properties and performance was investigated. Chemical composition and surface morphology of the prepared GO and membranes were analyzed by thermogravimetric analysis (TGA), Raman spectroscopy, FTIR spectroscopy, X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), and transmission electron microscopy (TEM). The fabricated composite membranes exhibited a significant increase in permeance (from 1.12 to 1.93 L m−2 h−1 bar−1) and salt rejection for Na2SO4 (from 95.9 to 98.9%) and NaCl (from 46.2 to 61.7%) at 2000 ppm, when compared to non-modified membranes. The amine- and acyl chloride-functionalized GO showed improved dispersibility in the respective phase.