The nanoscale structures of multilayer metal-phosphonate thin films prepared via a layer-by-layer assembly process using Zr(4+) and 1,12-dodecanediylbis(phosphonic acid) (DDBPA) or porphyrin square bis(phosphonic acid) (PSBPA) were studied using specular X-ray reflectivity (XRR), X-ray fluorescence, and long-period X-ray standing wave (XSW) analysis. The films were prepared in 1, 2, 3, 4, 6, and 8 layer series on both Si(001) substrates for XRR and on 18.6 nm period Si/Mo layered-synthetic microstructure X-ray mirrors for XSW. After functionalizing the SiO(2) substrate surfaces with a monolayer film terminated with phosphonate groups, the organic multilayer films were assembled by alternating immersions in (a) aqueous solutions containing Zr(4+)or Hf(4+) (final metal layer only) cations and then (b) organic solvent solutions of PO(3)-R-PO(3)(4-), where R was DDBPA or PSBPA spacer molecule. The Hf(4+) cation served as the marker for the top surface of the films, whereas the Zr(4+) cation was present in all other layers. The PSBPA also contained Zn and Re atoms at its midline which served as heavy-atom markers for each layer. The long-period XSW generated by the 0th- (total external reflection) through 4th-order Bragg diffraction conditions made it possible to examine the Fourier transforms of the fluorescent atom distributions over a much larger q(z) range in reciprocal space which permitted simultaneous analysis of Hf, Zn/Re, and Zr atomic distributions.