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A novel and effective green system consisting of deep eutectic solvent (DES) was proposed to prepare lignin nanoparticles (LNPs) without any lignin modification. The LNPs are obtained through the dialysis of the kraft lignin-DES solution. The particle size distribution, Zeta potential and morphology of the LNPs are characterized by using dynamic light scattering (DLS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The average diameter of LNPs is in the range 123.6 to 140.7 nm, and the LNPs show good stability and dispersibility in water. The composite beads composed of LNPs and sodium alginate (SA) are highly efficient (97.1%) at removing methylene blue (MB) from the aqueous solution compared to 82.9% and 77.4% by the SA/bulk kraft lignin composite and pure SA, respectively. Overall, the LNPs-SA bio-nanocomposite with high adsorption capacity (258.5 mg/g) could be useful in improving water quality and other related applications.