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ABSTRACT Intermittent streams are prevalent worldwide, yet the understanding of drivers of their changing flow patterns remains incomplete. We examined hydrological changes spanning four decades (1982–2020) in Kings Creek, an intermittent grassland stream within the Konza Prairie Biological Station in Kansas, USA. We analysed streamflow data from a US Geological Survey gauge on Kings Creek and three upstream Long Term Ecological Reasearch (LTER) sub‐watersheds with annual, biennial or quadrennial burn frequencies and linked trajectories of woody encroachment to increased evapotranspiration and changes in streamflow. Riparian woody cover doubled in the annually and biannually burned sub‐watersheds and sevenfold in the quadrennially burned watersheds. We observed significant decreases (84%) in daily discharge and number of annual flow days (55%) at the downstream USGS Kings Creek gauge, with similar changes in the LTER sub‐watersheds. The changing riparian cover, propelled by the regional expansion of woody plants, contributed to decreased streamflow by amplifying actual evapotranspiration (ET). Seasonal assessments underscored the critical influence of late summer conditions (July–September), under which increases in ET were linked to rising temperatures and increased evapotranspiration by riparian cover. Our results highlight the significant hydrological impacts of woody encroachment in grasslands and emphasize the importance of long‐term ecohydrological monitoring in unravelling the interplay between climate and vegetation as controls on the hyper‐variable flow patterns in this intermittent stream. Predicting and managing hydrological impacts on the flow of intermittent grassland rivers and streams worldwide requires accounting for the effects of accelerating woody encroachment.