A reliability analysis model for studying the influence of joint distribution of wave heights and periods on wave run-up and considering the fluctuation of water level is presented in this paper. Based on the definition of failure mode related to wave run-up, a reliability function may be formulated straightforwardly. In particular, the reliability analysis model can be directly taken into account the statistical properties and distributions of wave periods by treating the wave period in the reliability function to be a random variable. Also, the behaviour of wave height distribution conditioned to mean wave periods can be taken into account properly. It is found from the sensitivity analysis that the probabilities of failure of wave run-up is more dependent on the wave height than other variables such as seaside slope of structure. Additionally, it may be concluded that the effect of spectral bandwidth parameter on reliability index may be negligible. However, the effect of wave periods on the probability of failure of wave run-up may be indirectly appeared through the distribution of wave heights conditioned to the mean wave period. Finally, we can estimate the probabilities of failure with respect to the crest freeboard of rubble-mound breakwater, by which the optimal design of crest freeboard of rubble-mound breakwaters may be possible.