A novel Orr-Sommerfeld-like equation for gravity-driven turbulent open-channel flows over a granular erodible bed is here derived, and the linear stability analysis is developed. The whole spectrum of eigenvalues and eigenvectors of the complete generalized eigenvalue problem is computed and analyzed. The fourth-order eigenvalue problem presents singular non-polynomial coefficients with non-homogenous Robin-type boundary conditions that involve first and second derivatives. Furthermore, the Exner condition is imposed at an internal point. We propose a numerical discretization of spectral type based on a single-domain Galerkin scheme. In order to manage the presence of singular coefficients, some properties of Jacobi polynomials have been carefully blended with numerical integration of Gauss-Legendre type. The results show a positive agreement with the classical experimental data and allow one to relate the different types of instability to such parameters as the Froude number, wavenumber, and the roughness scale. The eigenfunctions allow two types of boundary layers to be distinguished, scaling, respectively, with the roughness height and the saltation layer for the bedload sediment transport.