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Since 2013, extreme floods within the Santee River basin (North/South Carolina, USA) caused $1.5B in damage. The instrumental period, however, is too short to determine if recent extreme events are anomalous within a long‐term context. Here, we present reconstructions of storm‐, base‐, and total streamflow for the Santee River using a multi‐species tree‐ring network calibrated to flow data during the period 1923–2018. Tree‐ring data explained higher variance (r = 0.59; p < 0.01; 900–2018) of instrumental baseflow than total streamflow (r = 0.41; p < 0.01; 1500–2018) or stormflow (r = 0.26; p < 0.05; 1690–2018). Our reconstruction reveals a long‐term increase in baseflow over the past millennium. The North Atlantic subtropical high regulates baseflow in the Santee River (r = 0.45; p < 0.01). Recent high levels of baseflow may be connected to the position of the subtropical high, increasing the likelihood of flooding. Plain Language Summary: Tree rings are often used to estimate past levels of streamflow to better place modern extremes into a historical context. Streamflow has two components, baseflow (flow from groundwater) and stormflow (flow contributed from storms). Here, we use tree rings to estimate past streamflow of the Santee River, South Carolina, USA. We find that tree rings are better at representing variations in baseflow rather than stormflow. This connection to baseflow is likely because tree growth is related to long‐term changes in water supply throughout the growing season, and changes in baseflow are more likely to result in changes in annual growth. Additionally, we find that certain species are more sensitive to baseflow than others, with Taxodium distichum (bald cypress) being the most sensitive. We were able to reconstruct baseflow back 1,100 years and found that baseflows increased over this time. Higher levels of baseflow will result in larger flooding events, like the 2013 and 2019 events. The location of the western edge of a large atmospheric high pressure centered off the Atlantic Coast, the North Atlantic subtropical high, has a strong influence on baseflow levels and could explain the increasing trend in reconstructed baseflows. Key Points: Tree rings better represent baseflow compared to stormflow and total streamflowRapid 20th–21st century increases in baseflow escalate flooding susceptibility and are exceptional over the last 1,118 yearsRecent increases in baseflow are related to the position of the western flank of the North Atlantic subtropical high [ABSTRACT FROM AUTHOR]