The trade-off between membrane permeability and selectivity and membrane fouling, including both physical and bio-fouling, are major challenges that limit the practical application of nanofiltration (NF) membranes. In order to address these issues simultaneously, multifunctional membranes with maximized water permeability/salt selectivity and enhanced antifouling and antibacterial properties are desired. In this work, we prepare a novel multifunctional thin film nanocomposite (TFN) NF membrane by embedding cellulose nanocrystal/silver (CNC/Ag) nanocomposites into a polyamide layer. The CNC/Ag TFN NF membranes exhibit excellent properties by taking advantage of both CNCs, a highly hydrophilic, low-cost, bio-renewable, and environmentally friendly nanomaterial, and Ag nanoparticles, one of the most effective bactericidal materials. With the incorporation of only 0.01 wt% CNC/Ag nanocomposites, a high pure water permeability (25.4 L m⁻² h⁻¹ bar⁻) and a high rejection rate of Na₂SO₄ (99.1%) of the CNC/Ag TFN NF membrane can be achieved, respectively. Besides, the membrane also exhibits exceptional antifouling (flux recovery ratio reaches 92.6% for humic acid) and antibacterial performance (99.4% reduction of Escherichia coli viability). Ag⁺ leaching tests also demonstrate the good stability of Ag nanoparticles in the active thin-film layer of the CNC/Ag NF membranes. These findings have strong positive implications for the development of next-generation high performance NF membranes for water treatment.