The main objective of this work is to investigate the natural vibrations of a system of two thin (Kirchhoff–Love) plates surrounded by liquid in terms of the coupled Stochastic Boundary Element Method (SBEM), Stochastic Finite Element Method (SFEM), and Stochastic Finite Difference Method (SFDM) implemented using three different probabilistic approaches. The BEM, FEM, and FDM were used equally to describe plate deformation, and the BEM was applied to describe the dynamic interaction of water on a plate surface. The plate’s inertial forces were expressed using a diagonal or consistent mass matrix. The inertial forces of water were described using the mass matrix, which was fully populated and derived using the theory of double-layer potential. The main aspect of this work is the simultaneous application of the BEM, FEM, and FDM to describe and model the problem of natural vibrations in a coupled problem in solid–liquid mechanics. The second very important novelty of this work is the application of the Bhattacharyya relative entropy apparatus to test the safety of such a system in terms of potential resonance. The presented concept is part of a solution to engineering problems in the field of structure and fluid dynamics and can also be successfully applied to the analysis of the dynamics of the control surfaces of ships or aircraft.