Vinasse, a waste from the bioethanol industry, presents a crucial environmental challenge due to its high organic matter content, which is difficult to biodegrade. Currently, no sustainable alternatives are available for treating the amount of vinasse generated. Conversely, biopolymers such as cellulose, carboxymethylcellulose, and chitosan are emerging as an interesting alternative for vinasse control due to their flocculating capacity against several organic compounds. This study seeks to determine the thermodynamic behavior of in silico interactions among three biopolymers (cellulose, carboxymethylcellulose, and chitosan) regarding 15 organic compounds found in vinasse. For this, the Particle Mesh Ewald (PME) method was used in association with the Verlet cutoff scheme, wherein the Gibbs free energy (ΔG) was calculated over a 50 ns simulation period. The findings revealed that cellulose showed a strong affinity for flavonoids like cyanidin, with a maximum free energy of −84 kJ/mol and a minimum of −55 kJ/mol observed with phenolic acids and other flavonoids. In contrast, chitosan displayed the highest interactions with phenolic acids, such as gallic acid, reaching −590 kJ/mol. However, with 3-methoxy-4-hydroxyphenyl glycol (MHPG), it reached an energy of −70 kJ/mol. The interaction energy for flavonoid ranged from −105 to −96 kJ/mol. Finally, carboxymethylcellulose (CMC) demonstrated an interaction energy with isoquercetin of −238 kJ/mol, while interactions with other flavonoids were almost negligible. Alternatively, CMC exhibited an interaction energy of −124 kJ/mol with MHPG, while it was less favorable with other phenolic acids with minimal interactions. These results suggest that there are favorable interactions for the interfacial sorption of vinasse contaminants onto biopolymers, indicating their potential for use in the removal of contaminants from the effluents of the bioethanol industry.