Methodology for diffusion coefficient determination was applied on sandstone samples, using conservative non sorbing tracer. The results proved that methodology, through-diffusion cell design and GoldSim diffusion module can be used for sandstone samples in order to determine important migration parameters, necessary for transport model input. However, rock heterogeneity factor has to be taken into account in any case as it can potentially change rock properties, even within centimeter scale. Effective diffusion coefficient D e for rock samples was determined. The values fell into the range of 1.0–6.17 × 10−10 m2 s−1. Discrepancies in measured and simulated porosity were observed. Statistical analyses revealed that values of diffusion coefficient D e were in close interrelation to primary mineral (quartz) and cement forming minerals (kaolinite and organic matter).