To solve the equation for gravity-gyroscopic waves in a rectangular domain, the distinguished algorithm for the solution of the Cauchy problem for a second-order transient equation is proposed. This algorithm is developed by using the time-varying finite element method. The space derivatives in the gravity-gyroscopic wave equation are approximated with finite differences. The stability and accuracy of the method are estimated. The procedure for the implementation of the method is developed. The calculations were performed for determining the steady-state modes of fluctuations of the solutions of the gravity-gyroscopic wave equation depending on the problem parameters.