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Flooding affects ecosystems by transporting water and solutes across aquatic-terrestrial interfaces, removing nutrient and organic substrate limitations, and spurring biogeochemical activity. Few studies have considered the influence of flooding on surface water-groundwater interactions. This research examines the temporally variable water storage and exchange in a stream in the McMurdo Dry Valleys (MDV) of Antarctica, where diel flood pulses occur due to glacial melt. Several MDV streams display truncated discharge peaks, suggesting water storage between the source glacier and the gauging station. We tested the hypothesis that stream braids and subsurface water storage contribute to the difference between glacial melt and stream outflow hydrographs by constructing a coupled surface water routing and subsurface water flow model. This model routes water into stream braids at high flows and allows this water to infiltrate and return to the stream via subsurface flow paths as flows recede. Our simulation demonstrates the importance of surface-subsurface water interactions in controlling the hydrograph shape. Maximum simulated discharge was sensitive to storage parameters including aquifer depth and the flooding threshold, while minimum discharge was sensitive to hydraulic conductivity. Subsurface storage volume varied by 38% over a diel cycle and stream-subsurface exchange rates varied from 0 to 0.19 m(3) h(-1) m(-1), with exchange from the stream to the subsurface during high flows, and vice versa at low flows. These results underscore how unsteady flow can increase hyporheic interactions and ecosystem productivity, and provide support for maintaining natural stream morphology and flow regimes.