In previous work, molecular modeling was used to investigate how acidic and nitrogen-containing surface groups (SG) on an activated carbon (AC) model affect the adsorption of chlordecone (CLD) and β-hexachlorocyclohexane (β-HCH), considering the effects of pH and hydration. Interactions involving acidic SGs at neutral pH indicated chemisorption, while interactions with nitrogen basic SGs suggested physisorption. This study presents a theoretical investigation of the interactions between these pesticides and oxygenated SGs on AC. A coronene molecule with functional groups—specifically pyrone, chromene, or ketone at the edges was used as a simplified model of AC. The Multiple Minima Hypersurface methodology was employed to study the interactions between CLD and β-HCH with SGs on AC using the PM7 semi-empirical Hamiltonian. Further re-optimization of the obtained structures for pesticide-AC complexes was performed using Density Functional Theory. The Quantum Theory of Atoms in Molecules was applied to characterize the interaction types using the Nakanishi criteria. No interactions were observed at acidic pH for both pollutants, whereas dispersive interactions were found at neutral and basic pH, indicating a physisorption process. Molecular dynamics simulations were also conducted to illustrate these findings. Ultimately, our previous studies showed that the adsorption process of CLD and β-HCH on AC is more effectively enhanced with acidic SGs rather than basic SGs. Moreover, MD simulations of β-HCH and CLD pesticides at concentrations higher than their solubilities reveal aggregation in both pure aqueous solutions and those containing AC. Analysis of MD trajectories and RDFs shows that hydrophobic interactions lead to aggregation of these molecules. RDFs indicate that β-HCH aggregates more in the solution due to its lower solubility compared to CLD. This aggregation reduces pesticide adsorption on AC surfaces, with β-HCH showing a more significant decrease in adsorption, dropping by more than half. Similar effects were observed with other biochar models for both pesticides.