Abstract Desalination of nitrates from brackish water is prominent in the coastal areas due to excessive disposal of pesticides by agricultural industries. Nowadays, membrane processes are growing tremendously for the desalination of brackish water. In this context, polyurea (PU) could be a useful membrane material for the treatment of brackish water. The present work deals with the removal of nitrates from synthetic water using PU membranes by nanofiltration (NF) process. Polyurea thin film composite (PU-TFC) membranes were prepared by interfacial polymerization followed by thermal crosslinking and characterized using Fourier transformed infrared spectral (FTIR), X-ray diffraction (XRD), scanning electron microscopy– energy dispersion X-ray spectroscopy (SEM–EDS), Atomic force microscopy (AFM), thermogravimetric (TGA), and universal testing machine (UTM) for structural analysis, crystallinity, morphological, compositional, thermal and mechanical properties, respectively. Experimental studies were conducted on an NF pilot plant by varying operating pressure from 2 to 10 bar and feed nitrate concentration from 60 to 200 mg/L for evaluating PU membrane performance. Experimental observations revealed a maximum water flux of 30.6 L/m2 h and nitrate rejection of 97.2% at a pressure of 10 bar for feed containing 140 mg/L of nitrate. A mass transfer model was developed on the basis of solution–diffusion mechanism for a semi-batch NF process by considering cake enhanced concentration polarization model, for laminar flow with feed recycle, using a plate and frame membrane module. A generic semi-batch NF process model was integrated taking into account concentration polarization and fouling layer resistance. The integrated model was successfully compared with existing data in literature and could be used for process scale-up. Due to the merits of hydrophilicity, negative charge, high thermal and mechanical resistance, the PU membrane can be termed as a low cost, commercially viable and ecofriendly barrier for separation of nitrates.