While it is established that climate change and human activities (for example, urbanization, dams) alter streamflows, there exists considerable uncertainty regarding the relative magnitude of their contributions. Most studies have focused on annual flows and found trends to be dominated by climate. Here we compare trends in seasonal flow totals for 315 natural and 1,957 managed watersheds across North America over 60 years (1950–2009). We find an amplification of seasonal flow trends in 44% of the managed watersheds, while 48% of the watersheds exhibit flow dampening. The magnitudes of amplification (20–167%) and dampening (5–52%) are substantial and vary seasonally. Multivariate models reveal that while rainfall, slope and forest cover are the key drivers of seasonal trends in natural watersheds, canals, impervious areas and dam storage dominate the responses in managed watersheds. Our findings of human-driven seasonal flow alterations highlight the need to develop adaptation strategies that mitigate the associated negative impacts.