The nanoscale structure of multilayer metal/phosphonate thin films prepared via a layer-by-layer assembly process was studied using specular X-ray reflectivity (XRR), X-ray fluorescence (XRF), and long-period X-ray standing wave (XSW) analysis. After the SiO2 X-ray mirror surfaces were functionalized with a monolayer film terminated with phosphonate groups, the organic multilayer films were assembled by alternating immersions in (a) aqueous solutions containing Zr4+, Hf4+, or Y3+ cations and then (b) organic solvent solutions of PO3-R-PO3, where R was a porphyrin or porphyrin-square spacer molecule. The different heavy metal cations provided X-ray fluorescence marker layers at different heights within the different multilayer assemblies. The XSW measurements used a 22 nm period Si/Mo multilayer mirror. The long-period XSW generated by the zeroth-order (total external reflection) through fourth-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 than previously achieved.