Water is considered ubiquitous within the shale reservoirs and mainly stored in the hydrophilic clay minerals. The water distribution characteristics and its effect on pore structure are important for the gas-in-place of shale systems. In this work, water vapor adsorption on montmorillonite (Mt), kaolinite (Kaol) and illite (Il) were performed to investigate the behaviors of water adsorption on shale clay. Subsequently, the moisture-equilibrated samples were conducted with N2 gas-adsorption techniques to investigate the effect of adsorbed water on pore structure characteristics, such as apparent pore size distribution (APSD), N2 BET specific surface area (N2-BET SSA) and pore volume (PV). The results show that the water uptake isotherms of our samples have the sigmoidal-shaped profiles and GAB model provides a good fit for the adsorption behavior. In addition, The APSD curves under different relative humidity (RH) conditions have validated the condensation effect and indicated that the small pores (approximately smaller than 5nm) are blocked by the capillary water and will disappear on the APSD curves at RH of 98% while the large nanopores (>5nm) are covered with water film, these effects will lead dramatically decrease of N2-BET SSA. Taking Mt and Il samples as the examples, the N2-BET SSA has declined to 33.51% and 33.66% compared with the dry conditions when Sw approaches to 50%. Meanwhile, these effects also indicate that the gas storage for clay minerals is massively overestimating under dry condition, the contribution to methane adsorption might be negligible in the actual shale reservoir. •Water adsorption isotherms were applied to investigate the adsorption behaviors of water vapor on clay minerals.•APSD curves were measured with N2 gas-adsorption techniques to validate capillary condensation in small pores.•The water distribution is visually presented by comparing the APSD curves between dry and moist condition.•The impact of water on pore structure characteristics and methane adsorption capacity are analyzed.