<p>Organohalide-respiring bacteria encoding reductive dehalogenases have shown substantial potential for bioremediation of organohalogen-contaminated environments. However, limited reactivity towards emerging pollutants, particularly fluorinated organics, constrains the broader application of these enzymes. To elucidate the molecular basis of this limitation, we investigated ligand-recognition mechanisms of the chlorinated-ethene dechlorinase PceA using molecular dynamics simulations. We find that tetrachlorinated ligands are stably accommodated in the binding pocket, whereas tetrafluorinated ligands can form hydrogen bonds with polar residues and are preferentially stabilised in a sub-pocket away from the catalytic site. Binding free-energy analyses indicate that van der Waals interactions and nonpolar solvation are the primary driving forces for association, favouring higher degrees of chlorination and longer carbon chains, and are facilitated by multiple aromatic residues. By contrast, polar solvation consistently opposes binding, with Arg305 acting as an antagonistic residue. Notably, polar solvation becomes more favourable with increasing fluorination for halogenated methanes and ethenes. The present study can provide insight for the relationship between binding free energy and ligands with various level of fluorination/chlorination and carbon chain length. The identified driving energy for ligand binding can be useful for understanding the limitations of reductive dehalogenase towards organofluorinated compounds.</p>