Flooding in the Amazon basin is frequently attributed to modes of large-scale climate variability, but little attention is paid to how these modes influence the timing and duration of floods despite their importance to early warning systems and the significant impacts that these flood characteristics can have on communities. In this study, river discharge data from the Global Flood Awareness System (GloFAS 2.1) and observed data at 58 gauging stations are used to examine whether positive or negative phases of several Pacific and Atlantic indices significantly alter the characteristics of river flows throughout the Amazon basin (1979-2015). Results show significant changes in both flood magnitude and duration, particularly in the north-eastern Amazon for negative El Niño-Southern Oscillation (ENSO) phases when the sea surface temperature (SST) anomaly is positioned in the central tropical Pacific. This response is not identified for the eastern Pacific index, highlighting how the response can differ between ENSO types. Although flood magnitude and duration were found to be highly correlated, the impacts of large-scale climate variability on these characteristics are non-linear; some increases in annual flood maxima coincide with decreases in flood duration. The impact of flood timing, however, does not follow any notable pattern for all indices analysed. Finally, observed and simulated changes are found to be much more highly correlated for negative ENSO phases compared to the positive phase, meaning that GloFAS struggles to accurately simulate the differences in flood characteristics between El Niño and neutral years. These results have important implications for both the social and physical sectors working towards the improvement of early warning action systems for floods.