Color Doppler optical coherence tomography (CDOCT) is a noninvasive technique for simultaneous high spatial resolution (~20 aem) imaging and high velocity resolution (~500 aem/s) imaging flowmetry in living tissues. In this paper, we demonstrate a reconstruction method which overcomes fundamental limitations on Doppler flow mapping associated with both high- and low-speed imaging. This algorithm is successful in retaining the high velocity resolution of CDOCT while eliminating motion artifact caused by slow image acquisition in samples which exhibit repetitive motion. We demonstrate reconstruction of blood flow throughout a beating Xenopus laevis heart and surrounding vasculature using gated CDOCT reconstruction.