The adaptive time-stepping algorithm for Brownian simulation of solute diffusion in three-dimensional complex geometries previously developed by the authors of this paper was applied to heterogeneous three-dimensional polymer hydrogel structures. The simulations were performed on reconstructed three-dimensional hydrogels. The obstruction effect from the gel strands on water and diffusion of dendrimers with different sizes were determined by simulations and compared with experimental nuclear magnetic resonance diffusometry data obtained from the same material. It was concluded that obstruction alone cannot explain the observed diffusion rates, but an interaction between the dendrimers and the gel strands should be included in the simulations. The effect of a sticky-wall interaction potential with geometrically distributed residence times on the diffusion rate has been studied. It was found that sticky-wall interaction is a possible explanation for the discrepancy between simulated and experimental diffusion data for dendrimers of different sizes diffusing in hydrogels.