This article investigates the velocity field of a free-surface flow subjected to harmonic deformation of the channel bottom, progressing asymptotically from a flat initial state to a maximum amplitude. Assuming a uniform main flow with the primary velocity component transverse to the bed undulation, analytical solutions are obtained for the three velocity components and free surface distortion using the method of perturbations. The perturbation components of the velocity field, streamlines, and surface deformation depend on a dimensionless parameter that reflects the fluid inertia induced by bed deformation relative to viscous resistance. When viscous effects dominate, a monotonic decay of the perturbations from the bed to the free surface is observed. In contrast, when inertia dominates, the perturbations can exhibit an oscillatory behavior and introduce circulation cells in the plane normal to the main flow. The interplay between inertia and viscosity reveals scenarios where surface and bed deformations are either in or out of phase, influencing vertical velocity components. Figures illustrate these phenomena, providing insights into the complex dynamics of free-surface flows with harmonic bed deformation in the direction normal to the main flow, and amplitude growing with time. The results are limited to small deformations of the channel bottom, as imposed by the linearization of the momentum equations. Even so, to the best of the authors' knowledge, this problem has not been addressed before.