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Intermittent headwater streams are highly vulnerable to environmental disturbances, but effective management of these water resources requires first understanding the mechanisms that generate streamflow. This study examined mechanisms governing streamflow generation in merokarst terrains, a type of carbonate terrain that covers much of the central United States yet has received relatively little attention in hydrological studies. We used high-frequency sampling of precipitation, stream water, and groundwater during summer 2021 to quantify the contributions to streamflow from different water sources and characterize their short-term dynamics in a 1.2 km 2 merokarst catchment at the Konza Prairie Biological Station (Kansas, USA). Mixing calculations using stable water isotopes and dissolved ions indicate that streamflow is overwhelmingly contributed by groundwater discharge from thin (1–2 m) limestone aquifers, even during wet periods, when soil water and surface runoff are generally expected to be more important. Relationships between hydraulic heads in the aquifers and their contributions to streamflow differed early in the study period compared to later, after a major storm occurred, suggesting there is a critical threshold of groundwater storage that the bedrock needs to attain before fully connecting to the stream. Furthermore, contributions from each limestone unit varied during the study period in response to differences in their hydrogeological properties and/or their stratigraphic position, which in turn impacted both the length of streamflow and its composition. Taken together, we interpret that the subsurface storage threshold and variation in aquifer properties are major controllers of flow intermittency in merokarst headwater catchments. 

Non‐perennial streams, which lack year‐round flow, are widespread globally. Identifying the sources of water that sustain flow in non‐perennial streams is necessary to understand their potential impacts on downstream water resources, and guide water policy and management. Here, we used water isotopes (δ¹⁸O and δ²H) and two different modeling approaches to investigate the spatiotemporal dynamics of young water fractions (F_yw) in a non‐perennial stream network at Konza Prairie (KS, USA) during the 2021 summer dry‐down season, as well as over several years with varying hydrometeorological conditions. Using a Bayesian model, we found a substantial amount of young water (F_yw: 39.1–62.6%) sustained flows in the headwaters and at the catchment outlet during the 2021 water year, while 2015–2022 young water contributions estimated using sinusoidal models indicated smallerF_ywamounts (15.3% ± 5.7). Both modeling approaches indicate young water releases are highly sensitive to hydrological conditions, with stream water shifting to older sources as the network dries. The shift in water age suggests a shift away from rapid fracture flow toward slower matrix flow that creates a sustained but localized surface water presence during late summer and is reflected in the annual dynamics of water age at the catchment outlet. The substantial proportion of young water highlights the vulnerability of non‐perennial streams to short‐term hydroclimatic change, while the late summer shift to older water reveals a sensitivity to longer‐term changes in groundwater dynamics. Combined, this suggests that local changes may propagate through non‐perennial stream networks to influence downstream water availability and quality.