This work investigates the water permeability of alkali-activated materials (AAMs), which is one of the key transport properties beside the diffusivity to assess the material durability. The AAMs were produced from granulate blast furnaces slag (BFS) and metakaolin (MK) with various water/binder ratios of 0.35, 0.45, 0.55, and 0.75, 0.85, 0.95 for BFS and MK based AAMs, respectively. Herein, a direct method using a constant flow controlled by a syringe pump, which has been successfully applied on conventional concrete, was used to measure the permeability of the AAMs. Data was then compared with the OPC mortars with similar w/b ratios. The results reveal that the permeability of BFS activated mortars is comparable to the one of OPC mortars. Both BFS and MK based AMMs are highly sensible with the changes in w/b ratio. The higher the w/b ratio, the higher the permeability. The extent in changing permeability with w/b ratio is stronger for BFS compared to MK based AMMs. Furthermore, a correlation between water permeability and microstructure obtained by nitrogen adsorption of the investigated AAMs is highlighted, which indicates that the permeability of MK based mortars is mostly controlled by capillary pores, while gel pores significantly affect the permeability of BFS based mortars.