In the Amazon Basin, floodplain inundation is a key component of surface water dynamics and plays an important role in water, energy and carbon cycles. The Model for Scale Adaptive River Transport (MOSART) was extended with a macroscale inundation scheme for representing floodplain inundation. The extended model, named MOSART-Inundation, was used to simulate surface hydrology of the entire Amazon Basin. Previous hydrologic modeling studies in the Amazon Basin identified and addressed a few challenges in simulating surface hydrology of this basin, including uncertainties of floodplain topography and channel geometry, and the representation of river flow in reaches with mild slopes. This study further addressed four aspects of these challenges. First, the spatial variability of vegetation-caused biases embedded in the HydroSHEDS digital elevation model (DEM) data was explicitly addressed. A vegetation height map of about 1 km resolution and a land cover dataset of about 90 m resolution were used in a DEM correction procedure that resulted in an average elevation reduction of 13.2 m for the entire basin and led to evident changes in the floodplain topography. Second, basin-wide empirical formulae for channel cross-sectional dimensions were refined for various subregions to improve the representation of spatial variability in channel geometry. Third, the channel Manning roughness coefficient was allowed to vary with the channel depth, as the effect of riverbed resistance on river flow generally declines with increasing river size. Lastly, backwater effects were accounted for to better represent river flow in mild-slope reaches. The model was evaluated against in situ streamflow records and remotely sensed Envisat altimetry data and Global Inundation Extent from Multi-Satellites (GIEMS) inundation data. In a sensitivity study, seven simulations were compared to evaluate the impacts of the five modeling aspects addressed in this study. The comparisons showed that representing floodplain inundation could significantly improve the simulated streamflow and river stages. Refining floodplain topography, channel geometry and Manning roughness coefficients, as well as accounting for backwater effects had notable impacts on the simulated surface water dynamics in the Amazon Basin. The understanding obtained in this study could be helpful in improving modeling of surface hydrology in basins with evident inundation, especially at regional to continental scales.