This paper documents the results of a study on the relationship of the pore structure and the transport properties of potassium- and sodium-based geopolymers. The pore structure was investigated by water porosity, mercury intrusion porosimetry and thermoporometry. The geopolymers transport properties were determined using a set of experiments, including natural diffusion of tritiated water and two electrical methods (direct current and Electrochemical Impedance Spectrometry). The geopolymers microstructure corresponds to materials with a pore structure made of poor access dimensions around 7 nm (potassium-based geopolymers), and 20 nm (sodium-based geopolymers) connected to larger pores not detected by MIP but revealed by thermoporometry. As a result, the transport properties appear to be higher than expected.