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The Mekong River is the most important river in Southeast Asia. It has increasingly suffered from water-related problems due to economic development, population growth and climate change in the surrounding areas. In this study, we built a distributed Geomorphology-Based Hydrological Model (GBHM) of the Mekong River using remote sensing data and other publicly available data. Two numerical experiments were conducted using different rainfall data sets as model inputs. The data sets included rain gauge data from the Mekong River Commission (MRC) and remote sensing rainfall data from the Tropic Rainfall Measurement Mission (TRMM 3B42V7). Model calibration and validation were conducted for the two rainfall data sets. Compared to the observed discharge, both the gauge simulation and TRMM simulation performed well during the calibration period (1998-2001). However, the performance of the gauge simulation was worse than that of the TRMM simulation during the validation period (2002-2012). The TRMM simulation is more stable and reliable at different scales. Moreover, the calibration period was changed to 2, 4, and 8 years to test the impact of the calibration period length on the two simulations. The results suggest that longer calibration periods improved the GBHM performance during validation periods. In addition, the TRMM simulation is more stable and less sensitive to the calibration period length than is the gauge simulation. Further analysis reveals that the uneven distribution of rain gauges makes the input rainfall data less representative and more heterogeneous, worsening the simulation performance. Our results indicate that remotely sensed rainfall data may be more suitable for driving distributed hydrologic models, especially in basins with poor data quality or limited gauge availability.