The present study investigates the nonlinear random vibration of the deep-water pier exposed to horizontal seismic excitation. First of all, the stochastic dynamic model of the pier is formulated. During the process, the pier is simplified as a cantilever beam fixed on the rock foundation, the seismic excitation is treated as Gaussian white noise, the hydrodynamic pressure is described with the radiation wave theory, and the equation for the nonlinear kinematic of the pier is deduced by the means of Kane’s method. Then, with the application of the stochastic averaging (SA) technique, the Fokker–Plank–Kolmogorov (FPK) equation governing the transient probability density function (PDF) of the amplitude envelope and the backward Kolmogorov (BK) equation for the conditional reliability function (CRF) are derived, respectively. The closed-form stationary PDF can be yielded directly from the reduced FPK equation, while the CRF and the conditional PDF of first-passage time are given after solving the BK equation numerically. Numerical discussions are performed to illustrate the trend of excitation intensity, mass ratio, immersion ratio, and inner and outer hydrodynamic effect on the stationary response and first-passage failure are examined, respectively. It has been shown that increases in the excitation intensity, mass ratio, and immersion ratio can amplify the response and reduce the reliability of the deep-water pier system. The hydrodynamic effect also leads to an amplification of the system response and a reduction in the reliability of the system. Similarly, the presence of inner water can also exacerbate these effects, and this phenomenon becomes more pronounced with increasing immersed ratios. Additionally, the analytical solution is validated by the result obtained by pertained Monte Carlo simulations (MCS). It is noted that this work will be helpful for the optimal seismic design of deep-water piers.