Different instabilities of the boundary layer flows that appear in the cavity between stationary and rotating discs are investigated using three-dimensional direct numerical simulations. The influence of curvature and confinement is studied using two geometrical configurations: (i) a cylindrical cavity including the rotation axis and (ii) an annular cavity radially confined by a shaft and a shroud. The numerical computations are based on a pseudo-spectral Chebyshev–Fourier method for solving the incompressible Navier–Stokes equations written in primitive variables. The high level accuracy of the spectral methods is imperative for the investigation of such instability structures. The basic flow is steady and of the Batchelor type. At a critical rotation rate, stationary axisymmetric and/or three-dimensional structures appear in the Bödewadt and Ekman layers while at higher rotation rates a second transition to unsteady flow is observed. All features of the transitions are documented. A comparison of the wavenumbers, frequencies, and phase velocities of the instabilities with available theoretical and experimental results shows that both type II (or A) and type I (or B) instabilities appear, depending on flow and geometric control parameters. Interesting patterns exhibiting the coexistence of circular and spiral waves are found under certain conditions.