Novel diffusion controlled delivery vehicles are among a host of recent developments in the micro and nano-encapsulation active ingredients in nutrition and biomedicine. Recently a technique for the synthesis of hollow biocompatible nanocapsules using layer-by-layer adsorption of oppositely charged polyelectrolytes was introduced. Here a method is presented to characterize the transport properties in these nanostructured materials and develop structure-property relationships between the membrane thickness, composition (i.e. chemical constituency), and synthesis conditions on the transport coefficients of the resulting nanocapsules. These variables are related to the transport properties via the mesh size of the polyelectrolyte membrane. Solute transport in the capsule membrane is measured via fluorescence recovery after photobleaching (FRAP). Coupled conservation equations are written in the nanomembrane and the capsule interior. The diffusion coefficient in capsule interior, D1, is measured by PFG-NMR. Data are presented for capsules synthesized from the polyanion poly-sodium 4-styrene sulfonate (PSS) and polycation poly-allylamine hydrochloride (PAH) that are 30nm and 50nm thick. For these capsules, unsteady transport of 66kDa TRITC-Dextran, which has a hydrodynamic radius of about 10 nm in solution, is measured. It is demonstrated that transport in both the capsule wall and interior must be considered, and that the value for D2, the transport coefficient in the capsule wall, is bounded between 1x10-15 m2/s and 1x10-14 m2/s.