Large volumes of wastewater containing different contaminants, including harmful heavy metals, have been produced as a result of the fast growth of the human population and worldwide industrialization. Although effective for this purpose, the use of adsorption is constrained by the high cost of adsorbent materials, thus calling for the need to develop economical water purification materials. This research prepared a low-cost nano bio-adsorbent from SCB-based nanocrystals and incorporated MIONPs, for the adsorption of Cr(VI) ions from aqueous media. The prepared adsorbent cellulose nanocrystal—magnetic Fe₃O₄ nanocomposite (CNCs-MIONPs) exhibited excellent adsorption efficiency at an optimal pH of 2, a pollutant initial concentration of 0.5 mg/L, a contact time of 90 min, and a shaking rate of 250 rpm. The highest efficiency possible was 91.78%. The greater surface area of the nanocomposite, together with its smaller particle size and active sites, provided areas for chromium species immobilization linked to increased chromate ion removal. Furthermore, the CNCs-MIONPs have a surface charge that can interact with the chromium species via electrostatic interactions at lower pH levels, increasing removal effectiveness. The pseudo-second model was the rate-limiting phase, and chemisorption involving valence forces via electron sharing or exchange between the sorbet and adsorbate occurred, offering the best correlation of the data. The modification of CNCs with MIONPs improved the adsorbents’ sorption efficiency. This offers great potential application in domestic and industrial water treatment plants.