Water saturation is one of the most important parameters in petroleum exploration and development. However, its calculation has been limited by the insufficient logging data required by a new technique that further influences the calculation of the free gas content. The accuracy of water saturation estimates is also a critical issue because it controls whether or not we can obtain an accurate gas saturation estimate. Organic matter plays an important role in shale-gas reservoirs, and the total organic carbon (TOC) indirectly controls the gas content and gas saturation. Hence, water saturation is influenced by inorganic and organic components. After analyzing the relationship among TOC, core water saturation, and conventional gas saturation, considering the influence of TOC on gas saturation in organic-rich shale reservoirs, we developed two new methods to improve the accuracy of water saturation estimates: the revised water saturation-TOC method and the water saturation separation method, in which Archie water saturation, modified total shale water saturation, and TOC are integrated. According to case studies of Longmaxi-Wufeng shale, southeastern Sichuan Basin, China, the water saturation results from these two methods in shale reservoirs with different lithologies are consistent with those from core analysis. We concluded that these two methods can be evaluated quickly and they effectively evaluate the water saturation of shale reservoirs.