Elution of poly(ethylene glycol) of molecular weight 200-20,000 Da from a size exclusion chromatography column packed with phenol-fed aerobic granules of three different nominal sizes (types I-III) has been investigated. The pore sizes of the three types of granules were evaluated based on the mean hydraulic times of the elution curves that decreased directly proportional to the increased logarithm of the molecular mass of a standard tracer and increased as granule size decreased. The corresponding exclusion limits for types I-III granules were 139,000, 123,000, and 54,500 Da, respectively. A one-dimensional convection-dispersion model described the effective dispersion coefficients of the tracers through the granule column. The intra-granular permeabilities and convective and diffusional transit times through the granule interior were evaluated by a dual porosity model. For small molecules of molecular mass < 5,000 Da, intra-granular convection dominated transport mechanisms at fast moving velocity. For comparatively larger molecules, diffusion barrier existed to limit nutrient supply to the granules. The size exclusion test provided intra granular transport characteristics using detailed analysis on the elution data.