Direct numerical solutions of the three-dimensional time-dependent Navier-Stokes equation are presented for the evolution of three-dimensional finite-amplitude disturbances in the Stokes boundary layer. The basic flow is driven harmonically in time and the disturbances represent a departure from the basic state of the fluid. For fixed value of the fluid viscosity, instability is shown to be a function of the amplitude of oscillation of the basic flow, excitation frequency, and the channel wall geometry. Special attention is given to pressure gradient and surface wave driven flows. Conditions for instability and transition are outlined.