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Changes in streamflow extremes can affect the economy and are likely to impact the most vulnerable in society. Estimating these changes is crucial to develop rational adaptation strategies and to protect society. Streamflow data from 1106 gauges were used to provide a comprehensive analysis of change in eight different extreme indices. The modified trend-free prewhitening and the false discovery rate were used to account for serial correlation and multiplicity in regional analysis, issues shown here to distort the results if not properly addressed. The estimated proportion of gauges with significant trends in low and high flows was about 23% and 15%, respectively. Half of these significant gauges had more than 60 years of data and were associated with changes greater than 5% per decade. A clear spatial pattern was identified, where most increasing trends in both low and high flows were observed in Southern Brazil, and decreasing trends in the remaining regions, except for the , where a pattern is not clear, and the proportion of significant gauges is low. Results based only on gauges unaffected by reservoirs suggest that reservoirs alone do not explain the increasing trends of low flows in the southern regions nor the decreasing trends in high flows in the remaining hydrographic regions.