In the McMurdo Dry Valleys of Antarctica, glaciers are the source of meltwater during the austral summer, and the streams and adjacent hyporheic zones constitute the entire physical watershed; there are no hillslope processes in these systems. Hyporheic zones can extend several metres from each side of the stream, and are up to 70 cm deep, corresponding to a lateral cross‐section as large as 12 m², and water resides in the subsurface year around. In this study, we differentiate between the near‐stream hyporheic zone, which can be characterized with stream tracer experiments, and the extended hyporheic zone, which has a longer time‐scale of exchange. We sampled stream water from Green Creek and from the adjacent saturated alluvium for stable isotopes of D and ¹⁸O to assess the significance and extent of stream‐water exchange between the streams and extended hyporheic zones over long time‐scales (days to weeks). Our results show that water residing in the extended hyporheic zone is much more isotopically enriched (up to 11‰ D and 2·2‰ ¹⁸O) than stream water. This result suggests a long residence time within the extended hyporheic zone, during which fractionation has occurred owing to summer evaporation and winter sublimation of hyporheic water. We found less enriched water in the extended hyporheic zone later in the flow season, suggesting that stream water may be exchanged into and out of this zone, on the time‐scale of weeks to months. The transient storage model OTIS was used to characterize the exchange of stream water with the extended hyporheic zone. Model results yield exchange rates (α) generally an order magnitude lower (10⁻⁵ s⁻¹) than those determined using stream‐tracer techniques on the same stream. In light of previous studies in these streams, these results suggest that the hyporheic zones in Antarctic streams have near‐stream zones of rapid stream‐water exchange, where ‘fast’ biogeochemical reactions may influence water chemistry, and extended hyporheic zones, in which slower biogeochemical reaction rates may affect stream‐water chemistry at longer time‐scales.