The replacement of natural forests with agriculture is generally associated with modifications in the hydrological behavior of a basin. This is particularly notable in the tropics and subtropics. Southern Brazil is a region with extensive agricultural production, forest conservation, and a vast unexplored streamflow data despite substantial rainfall trends observed in recent decades. In this work, we explore trends in the streamflow regime in the majority of the monitored basins in Southern Brazil. Additionally, we evaluate if pristine forested basins and agricultural nonforested basins have significantly different streamflow responses to changes in rainfall. We analyzed annual averages, maxima, minima, and seasonality of a 36‐year data set (1975–2010) of 675 rainfall and 140 streamflow gauges. Results reveal that large trends are widespread in Southern Brazil, especially in basins with areas smaller than 10,000 km2. Changes in the rainfall regime did not directly translate into changes in the streamflow regime. Changes in the annual maximum flow of forested basins were not statistically significant even when the annual average and maximum rainfall increased significantly. Correlations between changes in rainfall and streamflow for two indices, namely, duration of low‐magnitude events and seasonality, were statistically significant (p < 0.05) only for agricultural basins. The results indicate a higher propagation of hydrological changes through anthropogenically modified systems, providing evidence that agricultural basins are more sensitive to changes in the rainfall regime.