The structure and the conformations of diuron and irgarol have been investigated from crystal structure analyses and Density Functional Theory (DFT) calculations. Significant changes in terms of conformer distribution are found according to the surroundings (gas phase or water). Irgarol appears expectedly as flexible from a conformational point of view, nine or eight conformers being identified in the isolated state and water, respectively. Natural Bond Orbital (NBO) analyses have been realised on the energetic minima to rationalise the conformational preferences. Molecular electrostatic potential calculations have been carried out to bring to light and rank the potential intermolecular interaction sites of the two biocides. The interaction potential of irgarol, essentially represented by the triazine nitrogen atoms and the NH groups, is found to be much more sensitive to the conformational preferences that the one of diuron, the N3 triazine being preferred as HB acceptor, in agreement with the crystallographic data available.