In this work, cellulose nanocrystals (CNC) derived from sawdust were successfully incorporated into a nanofiltration membrane produced by the interfacial polymerization of piperazine (PIP) and trimesoyl chloride (TMC). The characteristics of unmodified and CNC-modified membranes were investigated using scanning electron microscopy (SEM), Atomic Force Microscopy (AFM), zeta potential measurement, X-ray photoelectron spectroscopy (XPS), and contact angle measurement. The performance of the membranes in terms of nitrate removal and water flux was investigated using 60 mg/L of potassium nitrate solution in a dead-end test cell. The characteristics of the modified membrane revealed a more nodular structure, higher roughness, increased negative surface charge, and higher hydrophilicity than the pristine membrane, leading to nitrate rejection of 94%. In addition, the membrane gave an average water flux of 7.2 ± 1.8 L/m²/h/bar. This work implies that nanofiltration, a relatively low-pressure process compared to reverse osmosis, can be used for improved nitrate removal from drinking water using an NF membrane modified with sawdust-derived cellulose nanocrystals.