Cellulose nanofibers were covalently functionalized using diethylenetriamine penta (methylene phosphonic acid) and studied for the extraction of heavy metal ions. The surface-functionalized nanofibers showed a high adsorption capacity towards heavy metal ions as compared to bare nanofibers. The elemental composition and surface morphology of the prepared bio-adsorbent was characterized by X-ray photoelectron spectroscopy, attenuated total reflectance infrared spectroscopy, field emission scanning electron microscopy, and energy dispersive spectroscopy. The prepared material was studied to develop a column-based solid phase extraction method for the preconcentration of trace metal ions and their determination by inductively coupled plasma optical emission spectroscopy. The batch experimental data was well fitted to Langmuir adsorption isotherms (R2 > 0.99) and follows pseudo-second-order kinetics. The experimental variables such as sample pH, equilibrium time, column breakthrough, sorption flow rate, the effect of coexisting ions, and eluent type were systematically studied and optimized accordingly. The detection limit of the proposed method was found to be 0.03, 0.05, and 0.04 µg L−1 for Cu(II), Pb(II), and Cd(II), respectively. Certified Reference Materials were analyzed to validate the proposed method against systematic and constant errors. At a 95% confidence level, the Student’s t-test values were less than the critical Student’s t value (4.302). The developed method was successfully employed for the preconcentration and determination of trace metal ions from real water samples such as river water and industrial effluent.