In this study, we used a geographic information system (GIS), remote sensing products and a digital elevation model (DEM) to prepare and to test the existing data sources and algorithms for a distributed, physically based, hydrological model, incorporating the gauging stations of the national networks of the Amazon basin. Watershed delineation for the Amazon sub-basin system is a necessary first step in distributed hydrological modelling. The DEMs currently available for the Amazon basin are GTOPO30, which has a grid spacing of about 1 km, and SRTM, which can be freely obtained from the internet at a resolution of about 90 m. Each of these DEMs has different sources and consequently different kinds of uncertainties. We have tested the two DEMs, comparing the results obtained using both of them on different sub-basins within the Amazonian basin. The delineation of the sub-basins for the entire Amazonian basin, which is currently available on our project site (http://www.mpl.ird.fr/hybam/), has been obtained from the GTOPO30. With GTOPO30 alone, the D8 algorithm (which determines the direction of flow in eight neighbouring cells) does not always give the correct delineation of sub-basins corresponding to the gauging stations. This problem occurs mainly in the very flat areas of the region. One way to overcome this problem is to burn-in the DEM with a river network. The spatial precision of this river network must be compatible with that of the DEM, and homogeneous throughout the basin. We tested three river networks on the Negro River sub-basins. We found that a suitable river network could be extracted by digitising a JERS-1 mosaic image. The DEM GTOPO30 burned-in with the JERS-1 extracted river network made the correct distributed modelling of the Amazon gauged sub-basins possible by determining water transfer times within the basin. Copyright © 2009 John Wiley & Sons, Ltd.