The microscopic mechanism accounting for the self-healing attribute of aromatic ionene-forming hydrogels derived from 1,4-diazabicyclo [2.2.2]octane (DABCO) and N,N’-(x-phenylene)dibenzamide (x = ortho-/meta-/para-) is unknown. Interestingly, the self-healing property of such DABCO-containing hydrogels is largely dependent on the polymer topology, the ortho ionene being the only self-healable without adding oppositely charged species. In this work, Molecular Dynamics (MD) simulations have been conducted to evaluate the influence of the topology on ionene···ionene and ionene··water interactions, as well as their effect on the self-healing behavior. For this purpose, destabilized and structurally damaged models were produced for ionene hydrogels with ortho, meta and para topologies and used as starting geometries for simulations. These models were allowed to evolve without any restriction during MD production runs and, subsequently, the temporal evolution of ionene···ionene and water···ionene interactions was examined. Analysis of the results indicated that the ortho-isomer rapidly forms unique interactions that are not detected for other two isomers. Thus, in addition to the interactions also identified for the meta-and para-ionenes, the ortho-isomer exhibits the formation of strong intermolecular three-centered (N–)H⋯O (=C)⋯H (–N) hydrogen bonds, intramolecular planar sandwich π-π stacking interactions and Cl−···N+ electrostatic interactions. Furthermore, the amount of intermolecular π-π stacking interactions and the strength of water···polymer interaction are also influenced by the topology, favoring the stabilization of the ortho-ionene reconstituted hydrogels. Overall, the arrangement of the functional groups in the ortho topology favors the formation of more types of ionene···ionene interactions, as well as stronger interactions, than in the meta and para topologies.