In the present study the adsorption of iopamidol (a pharmaceutical compound used in soft tissues diagnostic imaging based on X-ray radiography) onto activated carbons was assessed, since this is an effective technology to remove pharmaceutical compounds that fail to be degraded in conventional wastewater treatments. Three sisal-based carbons prepared by chemical activation with KOH, and two commercial carbons, were selected in order to understand the role of the porous structure in the removal of iopamidol from aqueous phase. The kinetic and equilibrium adsorption results indicate that iopamidol is adsorbed in mesopores and also in larger micropores (supermicropores). The adsorption isotherms reflect a complex mechanism originating unusual two-step isotherms, which highlights the influence of the porous structure. As proven using conductivity measurements and computational calculations, iopamidol can be adsorbed as a single molecule or in the form of aggregates, filling either small or much larger pores in a discontinuous way. By conjugating the molecular dimensions of the iopamidol species and the micropore size distribution of the samples, it was demonstrated that the unusual two-step isotherms are related with the absence of pores with width between 1.2 and 2.0 nm.