Late Quaternary shallow biogenic gas reservoirs have been discovered and exploited in the Qiantang River (QR) estuary area, eastern China. The fall of global sea level during the Last Glacial Maximum resulted in the formation of the QR incised valley. From bottom to top, the incised valley successions can be grouped into four sedimentary facies: river channel facies, floodplain–estuarine facies, estuarine-shallow marine facies, and estuarine sand bar facies. All commercial biogenic gas pools occur in floodplain–estuarine sand bodies of the QR incised valley and its branches. The deeply incised valleys provided favorable conditions for the generation and accumulation of shallow biogenic gas. The clay beds that serve as the direct cap beds of the gas pools are mostly restricted within the QR incised valley, with burial depths ranging from 30 to 80 m, remnant thicknesses of 10–30 m, and porosities of 42.2–62.6%. In contrast, the mud beds cover the whole incised valley and occur as indirect cap beds, with burial depths varying from 5 to 35 m, thicknesses of 10–20 m, and porosities of 50.6–53.9%. The pore-water pressures of clay and mud beds are higher than that of sand bodies, and the difference can be as much as 0.48 MPa. The pore-water pressures of clay or mud beds can exceed the total pore-water pressure and gas pressure of underlying sand reservoirs. Shallow biogenic gas can be completely sealed by the clay and mud beds, which have higher pore-water pressure. The direct cap beds have better sealing ability than the indirect cap beds. Generally, the pore-water pressure dissipation time of clay and mud beds is conspicuously longer than that of sand beds. This indicates that the clay and mud beds have worse permeability and better sealing ability than the sand beds. However, once the gas enters the sand lenses, the pore-water pressure cannot release efficiently.