The relationship of the hydrological variability of the Rio Negro in Manaus and the dominant large-scale climate variability patterns for the 1902–2007 period is investigated using the quantile method and composite analyses. Variations of the Rio Negro Level (RNL) during its 3-month high (May to July—MJJ) and low (October to December—OND) phases are examined separately. The El Niño (La Niña) related maximum warming (cooling) in the central tropical Pacific during its mature and decaying stages modulates the atmospheric circulation in the tropics and displaces the Walker circulation cell eastward (westward), so that its sinking (rising) branch occurs over western Amazon and causes negative (positive) precipitation anomalies in this region. These anomalous climate conditions occur before the Rio Negro high phase (MJJ) and contribute to reduce (increase) the RNL and lead to a very low (very high) event in the river. On the other hand, the SST variability modes in the tropical Atlantic mainly during the transition from wet to dry season modulate the precipitation variations over western Amazon in OND. The very high events are more frequent after the 1960’s decade and the very low events, before the 1930’s decade. Therefore, the occurrence of these events contains a multidecadal scale variability. The results also indicate that the variations in the rainfall in western Amazon occur up to 9 months in advance and modulate the RNL in Manaus. The results presented here might be useful for monitoring purposes of the RNL.