Floods and droughts have recently worsened in the Fraser River Basin (FRB), British Columbia, causing significant impacts to western Canadian economy, ecosystems, and societal wellbeing, as well as the costliest natural disaster in the province’s history in 2021. These extreme events present a major management challenge since the FRB is susceptible to unregulated spring flood and summer drought events, even in the same year. Meanwhile observational streamflow datasets are both short and potentially forced by anthropogenic warming, providing an incomplete record of long-term natural hydrological variability. Here, we present the first multi-century, seasonally-resolved paired freshet and drought reconstructions for the Fraser Basin Headwaters, the primary driver of overall FRB discharge. By independently reconstructing spring freshet- and summer drought-season runoff, we overcome methodological limitations that precluded prior attempts to reconstruct total water-year runoff in this basin. The reconstructions more than double the length of existing hydrologic datasets, and are used to analyze the magnitudes, durations, and statistical probabilities of anomalously high and low runoff of the past 140 years. We find that high freshet-season flows have intensified, enhancing the risk of flooding in the event of coeval extreme precipitation and that the frequency and temporal clustering of both high freshet and low drought-season runoff has intensified in recent decades. Our new datasets suggest existing hydrologic data underestimate past and future extreme events, and signal managers and stakeholders should take more conservative approaches in adapting to future FRB conditions under climate change.