Climatic variability and land surface change have a wide range of effects on streamflow and are often difficult to separate. We analyzed long-term records of climate, land use and land cover, and re-constructed the water budget based on precipitation, groundwater levels, and water use from 1950 through 2010 in the Cimarron–Skeleton watershed and a portion of the Cimarron–Eagle Chief watershed in Oklahoma, an irrigation-intensive agricultural watershed in the Southern Great Plains, USA. Our results show that intensive irrigation through alluvial aquifer withdrawal modifies climatic feedback and alters streamflow response to precipitation. Increase in consumptive water use was associated with decreases in annual streamflow, while returning croplands to non-irrigated grasslands was associated with increases in streamflow. Along with groundwater withdrawal, anthropogenic-induced factors and activities contributed nearly half to the observed variability of annual streamflow. Streamflow was more responsive to precipitation during the period of intensive irrigation between 1965 and 1984 than the period of relatively lower water use between 1985 and 2010. The Cimarron River is transitioning from a historically flashy river to one that is more stable with a lower frequency of both high and low flow pulses, a higher baseflow, and an increased median flow due in part to the return of cropland to grassland. These results demonstrated the interrelationship among climate, land use, groundwater withdrawal and streamflow regime and the potential to design agricultural production systems and adjust irrigation to mitigate impact of increasing climate variability on streamflow in irrigation intensive agricultural watershed.