Computational tools of analysis were used on a set of synthetic chromone containing sulfonamide derivatives for evaluation of their enzyme inhibitory activity against Carbonic Anhydrase (CA) isozymes. GOLD docking software was utilized to dock the compounds against two human Carbonic Anhydrase (hCA) proteins; hCAII and hCA-IX. Differences in conformation and orientation of molecules within hCA-II and hCA-IX binding pockets were studied in detail which revealed that compounds with fluorine at R1 position and phenyl sulfonamide substituent at para position served as potent inhibitors against both proteins due to anomalous chemistry of fluorine atom. It was also noticed that the activity was decreased when sulfonamide moiety was shifted from para to meta position since it dragged the interacting specie of compounds away from Zn metal. Similarly, when substituents were replaced by F > Br > C2H5 > H, the activity declined due to the electronegativity effect. Binding interaction results against CA-IX seemed to be better than CA-II due to large binding cavity, predicting the more potent inhibitory activity against hCA-IX.