An approach combining molecular dynamics (MD) simulations and laboratory experiments was applied to provide new theoretical insights into the chemical structure of polyamide (PA) thin-film composite (TFC) membranes modified with graphene quantum dots (GQDs). Interaction energies, fractional free volumes, mean-square displacements, densities, and water diffusion coefficients were computed for PA and four likely chemical structures of the GQD-embedded PA membranes. These theoretical results aided with experimentally measured water fluxes allowed for determining the most likely structure of the GQD–PA membrane. The compatibility of the GQDs and PA chains was found to be due to the formation of hydrogen and covalent bonds to m-phenylenediamine units. The modified membrane has a higher water diffusivity but a lower overall free volume, compared to the pristine PA membrane. MD simulations in concert with laboratory experiments were found to provide a good understanding of the relationship between the microscopic characteristics and macroscopic transport properties of TFC membranes.