Cellulose nanofibers (CNF) are sustainable nanomaterials, obtained by the mechanical disintegration of cellulose, whose properties make them an interesting adsorbent material due to their high specific area and active groups. CNF are easily functionalized to optimize the performance for different uses. The hypothesis of this work is that hydrophobization can be used to improve their ability as adsorbents. Therefore, hydrophobic CNF was applied to adsorb hexavalent chromium from wastewater. CNF was synthetized by TEMPO-mediated oxidation, followed by mechanical disintegration. Hydrophobization was performed using methyl trimetoxysilane (MTMS) as a hydrophobic coating agent. The adsorption treatment of hexavalent chromium with hydrophobic CNF was optimized by studying the influence of contact time, MTMS dosage (0–3 mmol·g−1 CNF), initial pH of the wastewater (3–9), initial chromium concentration (0.10–50 mg·L−1), and adsorbent dosage (250–1000 mg CNF·L−1). Furthermore, the corresponding adsorption mechanism was identified. Complete adsorption of hexavalent chromium was achieved with CNF hydrophobized with 1.5 mmol MTMS·g−1 CNF with the faster adsorption kinetic, which proved the initial hypothesis that hydrophobic CNF improves the adsorption capacity of hydrophilic CNF. The optimal adsorption conditions were pH 3 and the adsorbent dosage was over 500 mg·L−1. The maximum removal was found for the initial concentrations of hexavalent chromium below 1 mg·L−1 and a maximum adsorption capacity of 70.38 mg·g−1 was achieved. The kinetic study revealed that pseudo-second order kinetics was the best fitting model at a low concentration while the intraparticle diffusion model fit better for higher concentrations, describing a multi-step mechanism of hexavalent chromium onto the adsorbent surface. The Freundlich isotherm was the best adjustment model.