We consider Euler equations with stratified background state that is valid for internal water waves. The solution of the initial‐boundary problem for Boussinesq approximation in the waveguide mode is presented in terms of the stream function. The orthogonal eigenfunctions describe a vertical shape of the internal wave modes and satisfy a Sturm‐Liouville problem. The horizontal profile is defined by a coupled KdV system which is numerically solved via a finite‐difference scheme for which we prove the convergence and stability. Together with the solution of the Sturm‐Liouville problem, the stream functions give the internal waves profile.