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.