The role of the chemical properties of Pharmaceutically Active Compounds (PhACs) in their sorption behaviour and consequently in their fate and mobility is of major environmental interest, but a comprehensive evaluation is still lacking. The sorption of nine PhAC molecules with distinct physico-chemical properties on soils and goethite was described using linear, Freundlich and Langmuir models and the relationship between the chemical structures of the compounds and the parameters of the adsorption was evaluated using redundancy analysis (RDA). The latter showed that the sorption of the pharmaceuticals was determined by the intrinsic chemical characteristics of the molecules, as shown by the 35% value of constrained variability. For the hydrophobic estrogens, E1, E2 and EE2, the logD value and the number of hydrogen bond sites were found to be the main controlling factors for adsorption, indicating that hydrophobic interaction and hydrogen bonding are the dominant sorption mechanisms. The π energy of the molecules also proved a very important parameter, governing the retention of PhACs in soils, especially in the case of carbamazepine, oxazepam and lamotrigine. The main controlling factor for ionic compounds, such as diclofenac sodium, tramadol or lidocaine, is the fraction of PhACs present as charged species, revealing the importance of Coulomb forces. The results of this study will allow semi-quantitative predictions to be made on how the molecular structure governs the sorption of PhACs and which sorption mechanism could be involved.