This paper is concerned with the natural vibration characteristics of a rectangular plate with a rectangular hole in contact with the water. The addressed problem was solved by using the Rayleigh-Ritz method combined with the Green function method. This study presents the numerical approach, numerical results and experimental results. In addition, the validity of the approximate formula which mainly depends on the so-called non-dimensionalized added virtual mass incremental factor and the natural mode shape change due to the presence of the water were investigated. Experiments were also carried out to validate theoretical results. The theoretical results are in good agreement with the experimental results. It was found that the effect of a square hole on the natural frequencies of the square plate in contact with water is different from the effect of a square hole on the natural frequencies of the square plate in air and the approximate formula can predict lower natural frequencies in water with a good accuracy.