Presented here is a model framework based on a land surface topography that can be represented with various degrees of resolution and capable of providing representative channel/floodplain hydraulic characteristics on a daily to hourly scale. The framework integrates two models: (1) a water balance model (WBM) for the vertical fluxes and stores of water in and through the canopy and soil layers based on the conservation of mass and energy, and (2) a routing model for the horizontal routing of surface and subsurface runoff and channel and floodplain waters based on kinematic and diffusion wave methodologies. The WBM is driven by satellite-derived precipitation (TRMM_3B42) and air temperature (MOD08_M3). The model's use of an irregular computational grid is intended to facilitate parallel processing for applications to continental and global scales. Results are presented for the Amazon Basin over the period Jan 2001 through Dec 2005. The model is shown to capture annual runoff totals, annual peaks, seasonal patterns, and daily fluctuations over a range of spatial scales (>1, 000 to < 4·7M km2). For the period of study, results suggest basin-wide total water storage changes in the Amazon vary by approximately + /− 5 to 10 cm, and the fractional components accounting for these changes are: root zone soil moisture (20%), subsurface water being routed laterally to channels (40%) and channel/floodplain discharge (40%). Annual variability in monthly water storage changes by + /− 2·5 cm is likely due to 0·5 to 1 month variability in the arrival of significant rainfall periods throughout the basin. Copyright © 2009 John Wiley & Sons, Ltd.