The influence of water on the pore system and gas desorption in shale remains an open question that is not yet fully understood. In this study, we present the effect of water on the shale pore system and recovered desorbed gas through a series of measurements on shale samples. We utilized the Brunauer-Emmett-Teller (BET) low pressure N2 adsorption and Field Emission Scanning Electron Microscopy (FE-SEM) to observe and analyze the effects of water immersion and moisture on the pore system of shale samples from Batu Gajah (BG) and Kroh shale formations in Malaysia. The impact of water on desorption was then measured using the United States former Bureau of Mines (USBM) modified method. The results showed that the micropore and mesopore volumes of the Batu Gajah (BG) and Kroh (KH) shale samples were reduced by 64.84 and 44.12, respectively, after the samples were immersed in water. The BET-specific surface area declined by 88.34 and 59.63 for the BG and KH sample, respectively. Desorption results showed that the methane desorbed volume was (KH: 1.22 cc/g, BG: 0.94 cc/g) for the water immersed sample, and (KH: 0.72 cc/g, BG: 0.60) for the equilibrated sample. The difference can be attributed to the proportion of the organic (total organic carbon) and inorganic (clay) content found in the two shale samples. The total organic carbon (TOC) existing in the KH sample was 12.1 wt , which was greater than the organic carbon content of the BG sample (2.1 wt ). The clay content was found to be more dominant in the BG shale when compared to the KH shale. © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).