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The mixture of water and gas is treated as a homogeneous fluid. Based on Boit’s theory, the influences of water saturation on the dynamic responses of a partially sealed tunnel are investigated in the frequency domain. By utilizing the continuous condition, the analytical solutions of the displacement, stress and pore water pressure of a partially sealed tunnel in the nearly saturated soil are derived subject to the harmonic load. On this basis, the influences of water saturation and permeability coefficient on the system responses are discussed by the numerical example. It is shown that the water saturation has a great influence on the stress and pore water pressure amplitudes. In addition, the permeability in the boundary of the tunnel is reasonably described by the permeability coefficient.