Water exists in shale gas reservoirs in the form of connate water and retained fracturing fluid. The nanoscale interaction between gas and water plays an important role in gas transport in shale nanopores. However, the research comprehensively focusing on gas-water transport in all pore types including organic pores, inorganic pores, and fractures is limited. In this work, we use a pore-scale model to study the influence of water on gas transport in shale nanopores. Shale pore structure of the model includes three organic pores, three inorganic pores, and one fracture. Because fluids have different transport behaviors in each sort of pore, a mathematical formulation is derived to describe fluid adsorption-desorption, diffusion, and flow (convection) in organic pores, inorganic pores, and fractures, respectively. The mathematical formulation is used in the model to simulate gas-water transport at a wide range of pressures and water saturations. The influence of water on gas transport is analyzed by comparing equivalent gas flow rate in two-phase cases and single-phase (gas) cases. Results indicate that the equivalent gas flow rate in two-phase cases is on average 43.03% of the equivalent gas flow rate in single-phase cases. The impact of water mainly happens in the fracture due to mutual interference of gas and water during two-phase flow. This effect induces a linear relation between equivalent gas flow rate and water saturation. The two-phase flow in the fracture dominates gas transport capability in shales. The gas in inorganic pores has much better movability than the gas in organic pores under a limited pressure drop. In the case of water saturation 40% and average pressure 22 MPa, most of the gas in inorganic pores can transport out of the matrix, while over 54% of the gas in organic pores fails to transport out. This implies that shale gas production largely depends on free gas transport. Enhancing adsorbed gas recovery is essential to maintain good well productivity.