We propose a discrete-modulated continuous-variable measurement-device-independent quantum key distribution protocol over a fiber-to -water channel. Different from optical fiber, the underwater channel has more severe optical attenuation because of optical absorption and scattering, and it would reduce the maximum communication distance. To enhance the performance of the protocol, the photon subtraction operation is implemented at the modulator side. We carried out performance simulation in two different kinds of seawater channel, and the result shows that the scheme with photon subtraction has longer secure communication distance under certain conditions.