In many temperate streams, biological uptake of N acts to attenuate the transport of excess N from allochthonous anthropogenic imports. Relatively few studies have determined how this N uptake relates to the magnitude of physical vs. biological N storage in the stream corridor, especially for intermittent systems where allochthonous N imports are often low and N transport may only occur during brief periods of streamflow. Glacial meltwater streams in the McMurdo Dry Valleys of Antarctica provide an excellent setting to quantify autochthonous N cycling and storage processes supported by abundant algal mats and well-connected hyporheic zones. We combined historic point-scale sediment and periphyton sample datasets with remote sensing-based modeling of periphyton coverage to estimate how much N was stored in periphyton biomass and the hyporheic zone of a 5-km long McMurdo Dry Valley stream corridor (>100,000 m²). We contextualized these N storage calculations by estimating the magnitude of annual N imports to and exports from the stream corridor based on >2 decades of streamflow and surface water data, source glacier ice cores and meltwater data, and past studies of local aeolian deposition and biological N fixation rates. We found that in this highly oligotrophic system, stream corridor-scale N storage was ~1000x that of total annual N import or export fluxes. More than 90% of this temporarily stored N was autochthonous organic matter in the shallow (<10 cm) hyporheic zone, which acts as a reservoir that sustains N availability in the water column. Despite its location in a polar desert devoid of higher-order vegetation, area-normalized N storage (~40 g N/m²) was greater than that reported for streams at lower latitudes (~1–22 g N/m²). We also demonstrated that NH₄⁺ sorption to stream sediment may be an important physicochemical N storage mechanism that responds to short-term fluctuations in streamflow and governs the mobility of inorganic N. Altogether, this research illustrates the importance of quantifying N storage within stream corridors when evaluating the significance of internal cycling and physical retention processes that modulate N availability.