Understanding hydrological variability is of crucial importance for water resource management in sub-Saharan Africa (SSA). While existing studies typically focus on individual river basins, and suffer from incomplete records, this study provides a new perspective of trends and variability in hydrological flood and drought characteristics (frequency, duration, and intensity) across the entire SSA. This is achieved by: i) creating a 65-year long, complete daily streamflow dataset consisting of over 600 gauging stations; ii) quantifying changes in flood and drought characteristics between 1950 and 2014; iii) evaluating how decadal variability influences historical trends. Results of daily streamflow reconstructions using random forests provide satisfactory performance over most of SSA, except for parts of southern Africa. Using change-point and trend analyses, we identify-three periods that characterise historical variations affecting hydrological extremes in western and central Africa, and some parts of southern Africa: i) the 1950s–60s and after the 1980s–90s, when floods (droughts) tend to be more (less) intense, more (less) frequent and more (less) persistent; and ii) the 1970s–80s, when floods (droughts) are less (more) intense, less (more) frequent and less (more) persistent. Finally, we reveal significant decadal variations in all flood and drought characteristics, which explain aperiodic increasing and decreasing trends. This stresses the importance of considering multiple time-periods when analysing recent trends, as previous assessments may have been unrepresentative of long-term changes.