Remotely sensing data have advantages in filling spatiotemporal gaps of in situ observation networks, showing potential application for monitoring floods in data-sparse regions. By using the water level retrievals of Jason-2/3 altimetry satellites, this study estimates discharge at a 10-day timescale for the virtual station (VS) 012 and 077 across the midstream Yangtze River Basin during 2009–2016 based on the developed Manning formula. Moreover, we calibrate a hybrid model combined with Gravity Recovery and Climate Experiment (GRACE) data, by coupling the GR6J hydrological model with a machine learning model to simulate discharge. To physically capture the flood processes, the random forest (RF) model is employed to downscale the 10-day discharge into a daily scale. The results show that: (1) discharge estimates from the developed Manning formula show good accuracy for the VS012 and VS077 based on the improved Multi-subwaveform Multi-weight Threshold Retracker; (2) the combination of the GR6J and the LSTM models substantially improves the performance of the discharge estimates solely from either the GR6J or LSTM models; (3) RF-downscaled daily discharge demonstrates a general consistency with in situ data, where NSE/KGE between them are as high as 0.69/0.83. Our approach, based on multi-source remotely sensing data and machine learning techniques, may benefit flood monitoring in poorly gauged areas.