The geochemical and petrophysical characteristics of the Lower Paleozoic shales (the Lower Silurian Longmaxi Formation and the Lower Cambrian Niutitang Formation) in southern China have been well documented in recent years. However, the water content in these shales is less studied. Since water and hydrocarbons concomitantly distribute in the pore spaces of the shale reservoir, the water in the shale reservoir is important to the evaluation and development of its hydrocarbon resources. In the present study, the water content (C-IW) and equilibrium saturation (S-EW) of the two sets of overmature organic-rich shales, which were, respectively, collected from the Niutitang Formation of Fengye 1 well (FY1) and the Longmaxi Formation of Youqian 1 well (YQ1) in the Upper Yangtze Region of southern China, were investigated. The results show that the C-IW of the FYI and YQ1 shales is 4.17-5.29 mg/g and 3.70-5.06 mg/g, respectively; the S-EW of the FYI and YQ1 shales is 34.23-42.72% and 38.07-45.51%, respectively; and both sets of shales are in a subirreducible water-equilibrated state. The C-IW and C-EIW of these shales have positive correlations with their TOC content, total porosity, surface area, and pore volume of both the micropores and nonmicropores, but the S-EW has negative correlations with these parameters, indicating that the organic matter in these shales holds some water and that the TOC content mainly controls the C-IW, C-EIW, and S-EW. According to the regression lines in the TOC content vs C-IW plots and the TOC content vs C-EIW plots, the water equilibrium saturations of the organic-hosted pores (S-OW) and inorganic-hosted pores (SIB,) were estimated. The S-IW of these shales is greater than the S-OW, and the S-IW/S-OW, ratio of the FY1 and YQ1 shales is 2.28 and 2.04, respectively, quantitatively indicating that the organic-hosted pores of these overmature shales are less hydrophilic than the inorganic-hosted pores. Therefore, for a set of overmature shales (FY1 or YQ1), with increasing TOC contents, the organic-hosted pore content increases and provides more storage space for the water in the shales, but the bulk hydrophilia of the shales reduces, leading to an increase in the C-IW and C-EIW and a decrease in the S-EW.