Effective removal of colloidal particles such as bentonite clay remains a persistent challenge in industrial wastewater treatment due to their fine particle size, strong electrostatic stability, and high dispersibility. This study presents an innovative, non-destructive coagulation strategy using a Type III natural deep eutectic solvent (NADES) composed of L-arginine and glycerol (1:6 molar ratio) as a sustainable alternative to traditional coagulants. The NADES formulation was designed using COSMO-RS modeling to optimize hydrogen bonding interactions and confirmed through solid-liquid equilibrium (SLE) testing. FTIR analysis revealed significant shifts in hydroxyl and amine group vibrations in the NADES spectrum compared to the individual components, confirming strong intermolecular hydrogen bonding and eutectic formation. New peak broadening in the 3200–3400 cm⁻¹ range, along with band suppression around 1600 cm⁻¹, indicates effective interaction between L-arginine and glycerol at the molecular level. Zeta potential measurements confirmed the ability of the NADES to destabilize bentonite suspensions. The initial zeta potential of bentonite was approximately –32.6 mV, reflecting a highly stable colloidal state. Upon treatment with the L-arginine:glycerol NADES, the zeta potential increased significantly to +11.05 mV, indicating effective charge neutralization and reduced colloidal stability. This change was accompanied by a significant reduction in turbidity, formation of large visible flocs, and an average settling rate increase compared to the control. These results demonstrate that the NADES facilitates bentonite flocculation through electrostatic screening and hydrogen bonding, offering a gentler and biodegradable alternative to metal salts or synthetic polymers. VEGA QSAR modeling predicted low aquatic toxicity and high biodegradability, supporting its environmental compatibility for open-system applications. This novel NADES-based platform provides an effective, scalable approach for hybrid and modular water treatment systems, with potential utility in both industrial and municipal settings. The flocculated bentonite residue also offers opportunities for reuse in geopolymer or clay-composite building materials, aligning with sustainable material circularity goals.