The effect of flow rate modulation on low Reynolds number heat transfer enhancement in a transversely grooved passage was numerically simulated using a two-dimensional spectral element technique. Simulations were performed at subcritical Reynolds numbers of Rem = 133 and 267, with 20% and 40% flow rate oscillations. The net pumping power required to modulate the flow was minimized as the forcing frequency approached the predicted natural frequency. However, mixing and heat transfer levels both increased as the natural frequency was approached. Oscillatory forcing in a grooved passage requires two orders of magnitude less pumping power than flat passage systems for the same heat transfer level. Hydrodynamic resonance appears to be an effective method of increasing heat transfer in low Reynolds number systems where pumping power is at a premium, such as micro heat transfer applications.