A complex supramolecular process involving electrostatic and dispersion interactions, asphaltene aggregation is associated with detrimental petroleum deposition and scaling that pose challenges to petroleum recovery, transportation, and upgrading. The density functional ωB97X-D with a dispersion correction was employed to investigate supramolecular aggregates incorporating heterocycles dimers with 0, 1, 2, and 3 water molecules forming a stabilizing bridge connecting the monomers. The homodimers of seven heterocyclic model compounds, representative of moieties commonly found in asphaltene structures were studied: pyridine, thiophene, furan, isoquinoline, pyrazine, thiazole, and 1,3-oxazole. The contributions of hydrogen bonding involving water bridges spanning between dimers and π−π stacking to the total interaction energy were calculated and analyzed. The distance between the planes of the aromatic rings is correlated with the π-π stacking interaction strength. All the dimerization reactions are exothermic, although not spontaneous. This is mostly modulated by the strength of the hydrogen bond of the water bridge and the π-π stacking interaction. Dimers bridged by two water molecules are more stable than with additional water molecules or without any water molecule in the bridge. Energy decomposition analysis show that the electrostatic and polarization components are the main stabilizing terms for the hydrogen bond interaction in the bridge, contributing with at least 80% of the interaction energy in all dimers. The non-covalent interaction analysis confirms the molecular sites that have the strongest (hydrogen bond) and weak (π-π stacking) attractive interactions. They are concentrated in the water bridge and in the plane between the aromatic rings, respectively.