Nanocomposite polymeric hydrogels have potential to play an important role in clinical diagnostics, therapeutic agents, and electroanalytical devices, among other biotechnological applications. However, the relationship between nanocomposite structure (morphology) and transport specifically of proteins has not been systematically described. In this study, polyacrylamide (PAM) nanocomposites have been synthesized containing various compositions and aspect ratios of gold nanoparticles (GNP). These nanocomposite hydrogels have been characterized for morphology, and examined for their ability to change the effective electrophoretic mobility of a model protein, ovum serum albumin (OSA), under a low applied electric field of 6.7 V/cm. Addition of spherical (low aspect ratio) gold nanoparticles reduces the effective mobility of OSA, a result that cannot be explained by the lower effective cross-link density noted in swelling studies. However, the effective mobility of OSA can be predicted using simple tortuous path models, specifically the Lape-Cussler. An increase in aspect ratio of the nanoparticles produced further reductions in mobility, and this reduction was so significant that tortuous path contribution could not explain it. We expect that percolation of the higher aspect ratio gold nanoparticles (as seen in TEM images) led to preferred conduction through the gold network, and therefore resulted in lower mobility in the buffer. The structure mobility relationships found here help establish one possible regime for transport of proteins through nanocomposite hydrogels.