Terrestrial water storage in the Amazon basin and its surrounding areas is studied by exploring the instantaneous measurements of distance changes between two satellites from the GRACE mission. The surface water in the channels and floodplains can be significant in weighing total water storage. Its magnitude can be as large as soil moisture perturbing the motions of the satellites to a detectable amount by the on-board instrument. The river runoff routing simulations indicate the effective velocity throughout the Amazon basin over the years is about 30 cm/s with significant seasonal change. The lower velocity, during rising stages and peak water season, and the faster velocity, during falling stages, are delineated from the observations. The backwater effects may impact such seasonal change on the overall flow velocity. Direct assimilation of GRACE tracking data can contribute to land surface dynamic processes by resolving the time scale of transport in rivers and streams.