Fouling of contact lenses is often due to tear protein diffusion into and aggregation within the contact lens material. These processes can diminish water and oxygen diffusion and create optical cloudiness of the lens. In order to understand the interactions between proteins and hydrogel contact lens materials a study was designed to measure the diffusivity of two model proteins within hydrogel films of varying composition using fluorescence correlation spectroscopy (FCS). Diffusion of human serum albumin (HSA) and apoferritin (aFER) was examined in a range of ~20 μm thick poly(acrylamide) (pAA) and poly(2-hydroxyethyl methacrylate) (pHEMA) hydrogels. Protein diffusivity was measured as a function of depth position within each hydrogel film. The characteristic diffusion time for two proteins in pHEMA hydrogels increased relative to both their diffusivity in solution and in pAA hydrogels, indicating that the protein-pHEMA interaction rather than the degree of hydrogel crosslinking is responsible for the observed effects. The resulting spatial representation of the molecular diffusion of proteins into and interaction with hydrogel materials builds a basis on which to conduct similar studies using commercial contact lens samples.