Global Navigation Satellite System (GNSS) signals reflected at the water surface are received together with direct GNSS signals by two low-const receivers deployed to an unmanned aerial vehicle (UAV). From relative delay of the reflected signals with respect to the direct ones, the height of the UAV above the water surface can be determined by GNSS Reflectometry (GNSS-R). The height estimation is originally conducted independently for each epoch, but by forcing temporally continuous constraints on differences of two receiver clocks, estimates of whole epochs during the study period are then contributed in the recursive estimates of the height. Applying the new method to GNSS-R altimetry data during an approximately 3-min hovering period at around 120-m altitude, the mean and RMS differences from the measured and estimated heights become improved from 0.72 and 5.87 m to 0.35 and 3.74 m. The accuracy of measurements is also found strongly depends on elevation angles of GNSS satellites, and also is sensitive to contaminations of unexpected reflections such as from lands or ships.