Drilling and multi-stage hydraulic fracturing bring a large amount of water into the formation, and clay-bearing shale reservoirs interact with water, which may lead to reduction of gas production, attenuation of fracturing effects, and even wellbore instability. Because of the complex fabric of shale, a thorough understanding of changes in shale micromechanics and corresponding mechanisms when exposed to water remains unclear. In this work, representative terrestrial and marine shale samples were selected for experiments based on clay enrichment. Then, contact resonance (CR) technique was performed to characterize micromechanics of shale after exposure to water. Visual phenomena provided by environmental scanning electron microscopy (ESEM) assisted to explain the underlying mechanisms. It was found that the hydration effect lowered both the storage modulus and stiffness of samples, but with different contributions from brittle minerals and clay, as well as variations depending on bedding plane orientation. Owing to the difference in composition, terrestrial shale exhibited stronger water sensitivity and anisotropy, with a general 15%-25% decrease in modulus, while marine shale changed relatively little (-5%-15%). Moreover, microscopic observation experiments revealed that complex interaction mechanisms may have existed that produced the mechanical changes. The reduction of capillary force and the interlaminar swelling of clay particles after water adsorption weakened the strength-related behavior of shale. However, the swelling-caused confining effect or void space closure during the water imbibition process might have offset this weakening effect, and even increased mechanical properties. At mesoscale, excessive shrinkage caused the growth of micro-cracks, which significantly attenuated overall mechanical behavior.