The confluence phenomenon between the Rio Negro, with is black waters, and the Rio Solimões, with its suspended white sediments, is well known and attracts thousands of tourists every year near by the city of Manaus, Amazonas—Brazil. From this affluence point on, the Rio takes the legendary name of the Amazon River. In spite of the wide interest for this phenomenon, there are few studies concerning its hydrological functioning. A backwater effect takes place at the confluence, as the Solimões waters play the role of a hydraulic dam slowing down the Negro waters (Meade et al., 1991). The objective of this study is to narrow the knowledge gap by describing better this effect by hydro-acoustic measurement results on the 4 periods of hydrological cycle (2006/2007). The results in this text are supported by new discharge data now accessible. The data shows that the Rio Negro, whose levels are controlled by Rio Solimões water levels, has lower discharge in the period of water rise, than during the period of low water levels. This demonstrates a different dynamic between water discharge and water levels in that region. The data collected also helps distinguishing some of the main features from those two big rivers at different periods of the hydrological cycle: rising waters, flood peak, decreasing waters and low waters. The differences between these two rivers are emphasized mainly on parameters such as: flow velocities, water discharge and water slope. These differences still persists even considering the strong seasonality that controls the Amazon rivers hydrology.