The adsorption characteristic of methane in water-bearing shale is essential for the accurate estimation of shale gas reserves. The sorption mechanisms of moisture and methane in shale remain poorly understood. In this work, moisture equilibrium measurements in shales were conducted to study moisture absorption characteristics. The governing factors for moisture absorption were determined, and the suitability of moisture absorption models was evaluated. An innovative water saturation apparatus and an improved methane adsorption system were built to measure methane adsorption in high water-bearing shales. The suitability of the Langmuir model in describing methane adsorption in water-bearing shale was studied. A predictive model for methane adsorption in water-bearing shale was developed based on improved BP neural network algorithm, which was further utilized to determine the primary governing factors for methane adsorption. The results revealed that the equilibrated moisture content in shale presents a three-stage and S-type ascending trend with increasing relative humidity. The methane adsorption amount shows a slide-type downward trend with the increase of water content. The Peleg model demonstrates the superior performance in describing the hygroscopic isotherms, and the Langmuir model performs poorly in characterizing methane adsorption in shales with high water contents. The controlling factors for the ultimate moisture content mainly include specific surface area, average pore diameter, carbonate and pyrite content. The methane adsorption in water-bearing shale is mainly governed by water content and specific surface area. The results of this work enrich the understanding of the adsorption mechanisms of shale gas and provide a solid basis for the assessment of shale gas reserves.